Nucleoside reverse-transcriptase inhibitors (NRTIs), including stavudine (d4T), zidovudine (AZT), didanosine (ddI), zalcitabine (ddC), lamivudine (3TC) and abacavir (ABC), inhibit/terminate the reverse transcription of the HIV virus, and markedly improve life expectancy and quality of life in HIV-infected patients. This progress, however, has come at the price of frequent side effects. NRTIs can cause myopathy, cardiomyopathy, pancreatitis, peripheral neuropathy, lipodystrophy, hepatic steatosis, lactic acidosis and/or liver failure. Most of these adverse effects have been ascribed to the inhibition/termination of mitochondrial DNA (mtDNA) replication, thus depleting mtDNA. Among NRTIs, the so-called "D-drugs" (ddC, ddI, d4T) seem to be the most potent inhibitors of mitochondrial DNA polymerase γ and mtDNA replication. mtDNA depletion impairs the synthesis of mtDNA-encoded respiratory chain polypeptides. In turn, the depressed respiratory chain activity can secondarily inhibit fatty acid oxidation (FAO), pyruvate dehydrogenase and the tricarboxylic acid cycle, thus possibly leading to steatosis and lactic acidosis. The partial block in the flow of electrons also increases the generation of reactive oxygen species (ROS) by overly reduced respiratory chain complexes, and can also lead to cell death. Importantly, both the therapeutic effects of nucleoside analogues and their mtDNA-depleting action require their initial transformation into the triphosphate derivatives. This activation pathway competes with conjugation and/or degradation pathways. Exogenous and endogenous factors can diversely modulate these anabolic and catabolic pathways, to modulate antiretroviral efficacy and toxicity. Importantly, NRTIs can impair mitochondrial function and cell homeostasis without depleting mtDNA. Possible mechanisms could include the accumulation of oxidative lesions and mutations in mtDNA, drug-induced inhibition of the adenine nucleotide translocator, diverse effects on FAO enzymes and/or cofactors such as L-carnitine, and also genotoxic effects on nDNA. Some of these "mtDNA-unrelated" effects could disturb lipid homeostasis and participate to cell death in some tissues. Although it is still unclear why different nucleoside analogues tend to have different tissue-selective toxicities, and why some individuals may be more susceptible, recent data allow us to put forward some hypotheses.