Oetzi the Iceman, the name given to the frozen body discovered in the Alps in 1991, had a bacterial infection that is common today, researchers said.
He had been killed 5,300 years earlier after being struck by an arrow.
The research is published in the journal Science.
This new study suggests he was suffering from an infection that can cause stomach ulcers and gastritis.
A genetic analysis of the bacteria was carried out, helping to trace the history of the microbe, which is closely linked to the history of human migration.
The frozen corpse of Oetzi has allowed scientists to look back at his life in unprecedented detail.
Previous research has revealed that he was between 40 and 50 years old, had brown eyes, was covered in tattoos and had recently eaten ibex.
He was found with an arrow in his left shoulder, and most likely died of blood loss. However he also suffered other medical problems, including heel fractures, arthritis and possibly Lyme disease.
Now, to add to his health woes, scientists have now discovered the Helicobacter pylori bacteria.
The strain that infects Europeans today is thought to be the result of two older strains – one African and one Asian – combining.
Essentially this means infected people from these two areas must have come together and mixed.
However, the microbe found in Oetzi was different.
“We had assumed that we would find the same strain of Helicobacter in Oetzi as is found in Europeans today,” said Thomas Rattei, from the University of Vienna, in Austria, who worked on the study.
“It turned out to be a strain that is mainly observed in Central and South Asia today.”
This suggests that there may have been a wave of people from Africa, who were carrying the bacteria, into Europe at some point after Oetzi’s death.
It adds to the growing evidence that rather than a single movement of humans out of Africa and into Europe, there were several migrations.