Ötzi was found by two German tourists from Nuremberg, Helmut and Erika Simon, and excavated by German archaeologist Konrad Spindler on September 19, 1991; the body was at first thought to be a modern corpse, like several others which had been recently found in the region. Lying on its front and frozen in ice below the torso, it was crudely removed from the glacier by the Austrian authorities using a small jackhammer (which punctured the hip of the body) and ice-axes using non-archaeological methods. In addition, before the body was removed from the ice, people were allowed to see it, and some took portions of the clothing and tools as souvenirs. The body was then taken to a morgue in Innsbruck where its true age was ascertained.
Surveys in October 1991 showed that the body had been located 92.56 metres (101 yd) inside Italian territoryCoordinates: 46°46′44″N 10°50′23″E / 46.77889°N 10.83972°E. Since 1998 it has been on display at the South Tyrol Museum of Archaeology in Bolzano, Trentino-Alto Adige/Südtirol.
In 2001 X-rays and a CT scan revealed that Ötzi had an arrowhead lodged in his left shoulder when he died, and a matching small tear on his coat. The discovery of the arrowhead prompted researchers to theorize Ötzi died of blood loss from the wound, which would likely have been fatal even if modern medical techniques had been available. Further research found that the arrow's shaft had been removed before death, and close examination of the body found bruises and cuts to the hands, wrists and chest and cerebral trauma indicative of a blow to the head. One of the cuts was to the base of his thumb that reached down to the bone but had no time to heal before his death. Currently it is believed that death was caused by a blow to the head, though researchers are unsure if this was due to a fall, or from being struck with a rock by another person. Unpublished and thus unconfirmed DNA analyses claim they revealed traces of blood from four other people on his gear: one from his knife, two from the same arrowhead, and a fourth from his coat. Interpretations of these findings were that Ötzi killed two people with the same arrow, and was able to retrieve it on both occasions, and the blood on his coat was from a wounded comrade he may have carried over his back. Still, this is to be taken with caution. Ötzi's unnatural posture in death (frozen body, face down, left arm bent across the chest) suggests that the theory of a solitary death from blood loss, hunger, cold and weakness is untenable. Rather, before death occurred and rigor mortis set in, the Iceman was turned on to his stomach in the effort to remove the arrow shaft.

The DNA evidence suggests that he was assisted by companions who were also wounded; pollen and food analysis suggests that he was out of his home territory. The copper axe could not have been made by him alone. It would have required a concerted group tribal effort to mine, smelt and cast the copper axe head. This may indicate that Ötzi was part of an armed raiding party involved in a skirmish, perhaps with a neighboring tribe, and this skirmish had gone badly. When the Iceman's mitochondrial DNA was analyzed by Franco Rollo and his colleagues, it was discovered that he had genetic markers associated with reduced fertility. It has been speculated that this may have affected his social acceptance, or at least that his infertility could have had social implications within his tribal group, which could have played a role in the chain of events that led to the confrontation.