Combination of antiretroviral drugs has dramatically improved the prognosis of human HIV infection but is also associated with many adverse effects, the mitochondrial origin of which is discussed. In this study using extensive diagnostic procedures set up for inherited mitochondrial disorders, we analyzed HIV patients under active antiretroviral therapy who complained of severe adverse symptoms unexplained by HIV. All these patients had been treated for at least 5 years. They all had significant mitochondrial damage as evidenced by the diverse combination of lactate accumulation in blood or cerebrospinal fluid, mitochondrial morphologic alterations in muscle, and biochemical defects in muscle and liver, which designated mitochondrial DNA (mtDNA) as the main target of the toxic mechanisms. Southern blot and/or polymerase chain reaction -based analyses disclosed multiple deletions of the muscle mtDNA and reduction of the muscle and/or liver mtDNA copy number in a majority of the patients. In opposition to muscle and liver, blood mononuclear cells were devoid of significant biochemical or genetic alterations. Whether the mitochondrial toxicity is directly responsible for the patients' adverse symptoms remains disputable, because the investigations were transversal. Its severity argues for its clinical relevance, however. The skewed tissue distribution of mitochondrial alterations indicates potential pitfalls in the needed future prospective studies.