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The researchers in Berlin said the man, who suffered from leukaemia and HIV, had shown no sign of either disease since the transplant two years ago.
But they stressed it was an unusual case which needed further investigation.
Experts said the result may boost interest in gene therapy for HIV.
Berlin's Charite clinic said the 42-year-old patient was an American living in Berlin, but the man has not been identified.
The clinic said since the transplant was carried out 20 months ago, tests on the patient's bone marrow, blood and other organ tissues have all been clear.
However, this approach is not going to be an option for the majority of people who live with HIV, who are in sub-Saharan Africa.