In the fall of 1785, Scheele began to suffer from symptoms described as kidney disease. In early 1786, he also contracted a disease of the skin, which, combined with his kidney problems, so enfeebled him that he could foresee an early death. With that in mind, he married the widow of his predecessor, Pohl, two days before he died, so that he could pass undisputed title to his pharmacy and his possessions to her.
While Scheele's experiments generated substances which have long since been found to be hazardous, the compounds and elements he used to start his experiments were dangerous to begin with, especially heavy metals. Like most of his contemporaries, in an age where there were few methods of chemical characterisation, Scheele would smell and taste any new substances he discovered. Cumulative exposure to arsenic, mercury, lead, and their compounds and, perhaps, hydrofluoric acid, which he had discovered, as well as other substances, took their toll on Scheele. He died at the early age of 43, on 21 May 1786, at his home in Köping. Doctors said that he died of mercury poisoning.