Baltimore was born on March 7, 1938 in New York City to Gertrude (Lipschitz) and Richard Baltimore. Raised in the Queens neighborhoods of Forest Hills and Rego Park, Queens, he moved with his family to suburban Great Neck, New York while he was in second grade because his mother felt that the city schools were inadequate. His Father had been raised as an Orthodox Jew and his mother was an atheist, and Baltimore observed Jewish holidays and would attend synagogue with his Father through his Bar Mitzvah. He graduated from Great Neck North High School in 1956, and credits his interest in biology to a high-school summer spent at the Jackson Laboratory's Summer Student Program in Bar Harbor, Maine.

Baltimore earned his Bachelor's degree with high honors at Swarthmore College in 1960. He credits his interest in molecular biology to George Streisinger under whose mentorship he worked for one summer at Cold Spring Harbor Laboratory. Baltimore's Future promise was evident in his work as a graduate student when he entered MIT's graduate program in biology in 1960 with a brash and brilliant approach to learning science. His early interest in phage genetics quickly yielded to a passion for animal viruses. He took the Cold Spring Harbor course on animal virology in 1961 and he moved to Richard Franklin's lab at the Rockefeller Institute at New York City which was one of the few labs pioneering molecular research on animal virology. There he made fundamental discoveries on virus replication and its effect on cell metabolism, including the first description of an RNA replicase. He completed his PhD thesis work in 1964.

After his PhD, Baltimore returned to MIT for postdoctoral research with James Darnell in 1963. He continued his work on virus replication using poliovirus and pursued training in enzymology with Jerard Hurwitz at Albert Einstein College of Medicine in 1964/1965.

In February, 1965, Baltimore was recruited by Renato Dulbecco to the newly established Salk Institute for Biological Studies in La Jolla as an independent research associate. There he investigated poliovirus RNA replication and began a long and storied career of mentoring other scientists' early careers including Marc Girard, and Michael Jacobson. They discovered the mechanism of proteolytic cleavage of viral polyprotein precursors, pointing to the importance of proteolytic processing in the synthesis of eukaryotic proteins. He also met his Future wife, Alice Huang, who began working with Baltimore at Salk in 1967. He and Alice together carried out key experiments on defective interfering particles and viral pseudo types. During this work, he made a key discovery that polio produced its viral proteins as a single large polyprotein that was subsequently processed into individual functional peptides.

Baltimore was married in 1968 to Dr. Alice S. Huang. They have one daughter.

The discovery of reverse transcriptase, made contemporaneously with Howard Temin, who had proposed the provirus hypothesis, overturned the central dogma of molecular biology by showing that genetic information could traffic bidirectionally between DNA and RNA. They published these findings in back-to-back papers in the prestigious journal, Nature. This discovery was heralded as evidence that molecular and virological approaches to understanding cancer would yield new cures for the dreaded disease. This may have influenced President Richard Nixon's War on Cancer which was launched in 1971 and substantially increased research funding for the disease. In 1972, at the age of 34, Baltimore was awarded tenure as a Professor of Biology at MIT, a post that he held until 1997. In 1975, at the age of 37, Baltimore shared the Nobel Prize for Physiology or Medicine with Howard Temin and Renato Dulbecco. The citation reads, "for their discoveries concerning the interaction between tumor viruses and the genetic material of the cell." At the time, Baltimore's greatest contribution to virology was his discovery of reverse transcriptase.

After winning the Nobel Prize, Baltimore reorganized his laboratory, refocusing on immunology and virology, with immunoglobulin gene expression as a major area of interest. In 1973, he was awarded a prestigious American Cancer Society Professor of Microbiology that provided substantial salary support. Also in 1973, he became one of the early faculty members in the newly organized MIT Center for Cancer capping a creative and industrious period of his career with nearly fifty research publications including the paradigm-shifting paper on reverse transcriptase. The MIT CRC was led by Salvador E. Luria and quickly achieved pre-eminence with a remarkable group of faculty including Baltimore, Phillips Robbins, Herman Eisen, Philip Sharp, and Robert Weinberg, who all went on to illustrious research careers. Baltimore was honored as a Fellow of the American Academy of Arts and Sciences in 1974. He returned to New York City in 1975, for a year-long sabbatical at Rockefeller University working with Jim Darnell. In 1975, at the age of 37, he shared the Nobel Prize for Physiology or Medicine with Howard Temin and Renato Dulbecco. The citation reads, "for their discoveries concerning the interaction between tumor viruses and the genetic material of the cell." At the time, Baltimore's greatest contribution to virology was his discovery of reverse transcriptase (Rtase or RT) which is essential for the reproduction of retroviruses such as HIV and was discovered independently, and at about the same time, by Mizutani and Temin. Following this, his lab and intellectual interests expanded tackling new problems such as the pathogenesis of Abelson murine leukemia virus (AMuLV), lymphocyte differentiation and related topic in immunology. In 1980, his group isolated the oncogene in AMuLV and showed it was a member of a new class of protein kinases that used the amino acid tyrosine as a phosphoacceptor. This type of enzymatic activity was also discovered by Tony Hunter, who has done extensive work in the area. He also continued to pursue fundamental questions in RNA viruses and in 1981, Baltimore and Vincent Racaniello, a post-doctoral fellow in his laboratory, used recombinant DNA Technology to generate a plasmid encoding the genome of poliovirus, an animal RNA virus. The plasmid DNA was introduced into cultured mammalian cells and infectious poliovirus was produced. The infectious clone, DNA encoding the genome of a virus, is a standard tool used today in virology.

Baltimore is a member of the National Academy of Sciences USA (NAS), 1974; the American Academy of Arts and Sciences, 1974; the NAS Institute of Medicine (IOM), 1974; the American Association of Immunologists, 1984. He was elected a Foreign Member of the Royal Society (ForMemRS) in 1987; the French Academy of Sciences, 2000; and the American Association for Cancer Research (AACR). He is also a member of the Pontifical Academy of Sciences, 1978. In 2006 Baltimore was elected to a three-year term as President of the American Association for the Advancement of Science (AAAS).

Baltimore recently joined with other Scientists to call for a worldwide moratorium on use of a new genome-editing technique to alter inheritable human DNA. A key step enabling researchers to slice up any DNA sequence they choose was developed by Emmanuelle Charpentier, then at Umea University in Sweden, and Jennifer A. Doudna of the University of California, Berkeley. Reminiscent of the Asilomar conference on recombinant DNA in 1975, those involved want both Scientists and the public to be more aware of the ethical issues and risks involved with new techniques for genome modification.

During the late 1980s and early 1990s, Thereza Imanishi-Kari, a scientist who was not in Baltimore's laboratory but in a separate, independent laboratory at MIT, was implicated in a case of scientific fraud. The case received extensive news coverage and a Congressional investigation. The case was linked to Baltimore's name because of his scientific collaboration with and later his strong defense of Imanishi-Kari against accusations of fraud.

In 1982, with a charitable donation by businessman and philanthropist Edwin C. "Jack" Whitehead, Baltimore was asked to help establish a self-governed research institute dedicated to basic biomedical research. They devised a unique structure of an independent research institute composed of "members" with a close relationship with the Department of Biology of MIT. The Whitehead Institute for Biomedical Research (WIBR) was launched with $35 million to construct and equip a new building located across the street from the MIT cancer center in Cambridge Massachusetts. The institute also received $5 million per year in guaranteed income and a substantial endowment in his will (for a total gift of $135 million). Under Baltimore's leadership, a distinguished group of founding members including Gerald Fink, Rudolf Jaenisch, Harvey Lodish, and Robert Weinberg was assembled and eventually grew to 20 members in disciplines ranging from immunology, genetics, and oncology to fundamental developmental studies in mice and fruit flies. Whitehead Institute's contributions to bioscience have long been second to none. Less than a decade after its founding with continued leadership by Baltimore, the Whitehead Institute was named the top research institution in the world in molecular biology and genetics, and over a recent 10-year period, papers published by Whitehead Scientists were the most cited papers of any biological research institute.

As early as 1984, Rudolf Grosschedl and David Weaver, postdoctoral fellows, in Baltimore's laboratory, were experimenting with the creation of transgenic mice as a model for the study of disease. They suggested that "control of lg gene rearrangement might be the only mechanism that determines the specificity of heavy chain gene expression within the lymphoid cell lineage." in 1987, they created transgenic mice with the fused gene that developed fatal leukemia.

In 1986, while a Professor of Biology at MIT and Director at Whitehead, Baltimore co-authored a scientific paper on immunology with Thereza Imanishi-Kari (an Assistant Professor of Biology who had her own laboratory at MIT) as well as four others. A postdoctoral fellow in Imanishi-Kari's laboratory, Margot O'Toole, who was not an author, reported concerns about the paper, ultimately accusing Imanishi-Kari of fabricating data in a cover-up. Baltimore, however, refused to retract the paper.

David G. Schatz and Marjorie Oettinger, as students in Baltimore's research group in 1988 and 1989, identified the protein pair that rearranges immunoglobulin genes, the recombination-activating gene RAG-1 and RAG-2. this was a key discovery in determining how the immune system can have specificity for a given molecule out of many possibilities, and was considered by Baltimore as of 2005 to be "our most significant discovery in immunology".

Around October 1989, when Baltimore was appointed President of Rockefeller University, around a third of the faculty opposed his appointment because of concerns about his behaviour in the Imanishi-Kari case. He visited every laboratory, one by one, to hear those concerns directly from each group of researchers.

Baltimore served as the Director of the Whitehead Institute until July 1, 1990 when he was appointed the sixth President of Rockefeller University in New York City. He moved his research group to New York and continued to make creative contributions to virology and cellular regulation. He also begin important reforms in faculty management and promoted the status of junior faculty at the University. After resigning on December 3, 1991, Baltimore remained on the Rockefeller University faculty and continued research until spring of 1994. He then rejoined the MIT faculty as the Ivan R. Cottrell Professor of Molecular Biology and Immunology.

In a draft report dated March 14, 1991 and based mainly on USSS forensics findings, NIH's fraud unit, then called the Office of Scientific Integrity (OSI), accused Imanishi-Kari of falsifying and fabricating data. It also criticized Baltimore for failing to embrace O'Toole's challenge. Less than a week later, the report was leaked to the press. Baltimore and three co-authors then retracted the paper; Imanishi-Kari and Moema H. Reis did not sign the retraction. In the report, Baltimore admitted that he was "too willing to accept" Imanishi-Kari's explanations, and felt he "did too little to seek an independent verification of her data and conclusions." Baltimore publicly apologized for not taking a whistle-blower's charge seriously.

In July 1992, the US Attorney for the District of Maryland, who had been investigating the case, announced he would bring neither Criminal nor civil charges against Imanishi-Kari. In October 1994, however, OSI's successor, the Office of Research Integrity (ORI; HHS) found Imanishi-Kari guilty on 19 counts of research misconduct, basing its conclusions largely on Secret Service analysis of laboratory notebooks.

Baltimore has been both defended and criticized for his actions in this matter. In 1993, Yale University Mathematician Serge Lang strongly criticized Baltimore's behavior. Historian of science Daniel Kevles, writing after the exoneration of Imanishi-Kari, recounted the affair in his 1998 book, The Baltimore Case. Horace Freeland Judson also gives a critical assessment of Baltimore's actions in The Great Betrayal: Fraud In Science. Baltimore has also written his own analysis.

An HHS appeals panel began meeting in June 1995 to review all charges in detail. In June 1996, the panel ruled that the ORI had failed to prove even one of its 19 charges. After throwing out much of the documentary evidence gathered by the ORI, the panel dismissed all charges against Imanishi-Kari. As their final report stated, the HHS panel "found that much of what ORI presented was irrelevant, had limited probative value, was internally inconsistent, lacked reliability or foundation, was not credible or not corroborated, or was based on unwarranted assumptions." It did conclude that "The Cell paper as a whole is rife with errors of all sorts ... [including] some which, despite all these years and layers of review, have never previously been pointed out or corrected. Responsibility ... must be shared by all participants." Neither OSI nor ORI ever accused Baltimore of research misconduct. The reputations of Stewart and Feder, who had pushed for the investigation, were very damaged.

On May 13, 1997, Baltimore was appointed President of the California Institute of Technology (Caltech). He began serving in the office 15 October 1997 and was inaugurated 9 March 1998.

During Baltimore's tenure at Caltech, United States President Bill Clinton awarded Baltimore the National Medal of Science in 1999 for his numerous contributions to the scientific world. In 2004, Rockefeller University gave Baltimore its highest honor, Doctor of Science (honoris causa).

In October 2005, Baltimore resigned the office of the President of Caltech, saying, "This is not a decision that I have made easily, but I am convinced that the interests of the Institute will be best served by a presidential transition at this particular time in its history..." Soon after, at Baltimore's request, Caltech began investigating the work Luk van Parijs had conducted while a postdoc in Baltimore's laboratory. Van Parijs first came under suspicion at MIT, for work done after he had left Baltimore's lab. After van Parijs had been fired by MIT, his doctoral supervisor also noted problems with work van Parijs did at the Brigham and Women's Hospital, before leaving Harvard to go to Baltimore's lab. Concluding in March 2007, the Caltech investigation found van Parijs alone committed research misconduct and that four papers co-authored by Baltimore, van Parijs, and others required correction.