The method of identifying Criminals by their fingerprints had been introduced in the 1860s by Sir william James Herschel in India, and their potential use in forensic work was first proposed by Dr. Henry Faulds in 1880. Galton, following the idea written by Faulds, which he failed to credit, was the first to place the study on a scientific footing, which assisted its acceptance by the courts. The Japanese police officially adopted the fingerprinting system in 1911.

Following graduation, Faulds then became a medical missionary for the Church of Scotland. In 1871, he was sent to British India, where he worked for two years in Darjeeling at a hospital for the poor.

On 23 July 1873, he received a letter of appointment from the United Presbyterian Church of Scotland to establish a medical mission in Japan. He married Isabella Wilson that September, and the newlyweds departed for Japan in December.

Faulds established the first English mission in Japan in 1874, with a hospital and a teaching facility for Japanese medical students. He helped introduce Dr. Joseph Lister's antiseptic methods to Japanese Surgeons. In 1875, he helped found the Rakuzenkai, Japan's first society for the blind, and set up lifeguard stations to prevent drowning in nearby canals. He halted a rabies epidemic that killed small children who played with infected mice, and he helped stop the spread of cholera in Japan. He even cured a plague infecting the local fishmonger's stock of carp. In 1880 he helped found a school for the blind. By 1882, his Tsukiji Hospital in Tokyo treated 15,000 patients annually. Faulds became fluent in Japanese, and in addition to his full-time work as a Doctor, he wrote two books on travel in the Far East, many academic articles, and started three magazines.

In an attempt to promote the idea of fingerprint identification he sought the help of the noted naturalist Charles Darwin. Darwin declined to work on the idea, but passed it on to his relative Francis Galton, who forwarded it to the Anthropological Society of London. When Galton returned to the topic some eight years later, he paid little attention to Faulds' letter. As a result of this interchange some controversy has arisen about the Inventor of modern forensic fingerprinting. However, there can be no doubt that Faulds' first paper on the subject was published in the scientific journal Nature in 1880; all parties conceded this.

Returning to Britain in 1886, after a quarrel with the missionary society which ran his hospital in Japan, Faulds offered the concept of fingerprint identification to Scotland Yard but he was dismissed, most likely because he did not present the extensive evidence required to show that prints are durable, unique and practically classifiable. Subsequently, Faulds returned to the life of a police surgeon, at first in London, and then in the Stoke-on-Trent town of Fenton. In 1922 he sold his practice and moved to James Street in nearby Wolstanton where he died in March 1930 aged 86, bitter at the lack of recognition he had received for his work. In 2007 a plaque acknowledging Faulds' work was unveiled at Bank House, near to Wolstanton's St Margaret's churchyard where his grave can be seen. In 2011, a plaque was unveiled at his former James Street residence. On 12 November 2004 a memorial was dedicated to his memory in Beith town centre close to the site of the house in New Street where he was born.