As a result of McCrones work on the Vinland Map, British author and researcher Ian Wilson approached McCrone in 1974 about the possibility of scientifically analyzing the Shroud of Turin, a length of linen cloth that has been venerated for centuries as the burial shroud of Jesus upon which his image is miraculously imprinted.  This led to McCrones involvement with the Shroud of Turin Research Project (STURP).  In 1977, a team of scientists affiliated with STURP proposed a barrage of tests to be carried out on the Shroud.  With permission from the Archbishop of Turin, Cardinal Anastasio Ballestrero, STURP researchers conducted tests over a period of five days in October 1978, also using adhesive tape to obtain samples of the fibers from various parts on the Shroud's surface.
Based on his microscopic and chemical analysis of the tape samples obtained by STURP, McCrone concluded that the image on the Shroud was painted with a dilute pigment of red ochre in a collagen tempera (i.e., gelatin) medium, using a technique similar to the grisaille employed in the 14th century by Simone Martini and other European artists.  McCrone also found that the "bloodstains" in the image had been highlighted with vermilion (a bright red pigment made from mercury sulfide), also in a collagen tempera medium.  McCrone reported that no actual blood was present in the samples taken from the Shroud.
McCrones results were rejected by other members of STURP and McCrone resigned from STURP in June 1980.  Two other members of STURP, John Heller and Alan Adler, published their own analysis concluding that Shroud did show traces of blood.  Other STURP members also disputed McCrones conclusion that the Shroud image was painted, finding that physical analyses excluded the presence of pigments in sufficient quantities to account for the visible image.
McCrone continued to defend his results and to insist that polarized light microscopy, in which he was the only expert among the original members of STURP, was the correct technique to apply to the study of the Shroud.  In 1983 he confidently predicted that radiocarbon dating of the Shrouds linen would show that it had been made shortly before the first historically recorded exhibition of the Shroud in 1356.  The results of the 1988 radiocarbon dating of the Shroud vindicated McCrones microscopic and chemical analyses.
Until McCrones death in 2002, he continued to comment upon and explain the analysis that he had performed, becoming a prominent figure in the ongoing controversies surrounding the Shroud that attracted considerable attention in the public press.  He re-stated and summarized his evidence that the Shroud was painted in an article published in 1990 in the journal Accounts of Chemical Research.  He later wrote a book on the subject, Judgment Day for the Shroud of Turin, which was published in 1996 by the McCrone Research Institutes Microscope Publications and re-issued in 1999 by Prometheus Books ().  In 2000, the American Chemical Society presented  McCrone with its National Award in Analytical Chemistry for his work on the Shroud and for "his enduring patience for the defense of his methodologies."