BACKGROUND Some nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) combinations cause additive or synergistic interactions in vitro and in vivo. METHODS We evaluated the mitochondrial toxicity of tenofovir (TFV), emtricitabine (FTC) and abacavir as carbovir (CBV) alone, with each other, and in combination with additional NRTIs. HepG2 human hepatoma cells were incubated with TFV, FTC, CBV, didanosine (ddl), stavudine (d4T), lamivudine (3TC) and zidovudine (AZT) at concentrations equivalent to 1 and 10x clinical steady-state peak plasma levels (C(max)). NRTIs were also used in double and triple combinations. Cell growth, lactate production, intracellular lipids, mtDNA and the mtDNA-encoded respiratory chain subunit II of cytochrome c oxidase (COXII) were monitored for 25 days. RESULTS TFV and 3TC had no or minimal toxicity. FTC moderately reduced hepatocyte proliferation independent of effects on mtDNA. ddl and d4T induced a time- and dose-dependent loss of mtDNA and COXII, decreased cell growth and increased levels of lactate and intracellular lipids. CBV and AZT strongly impaired hepatocyte proliferation and increased lactate and lipid production, but did not induce mtDNA depletion. The dual combination of TFV plus 3TC had only minimal toxicity; TFV plus FTC slightly reduced cell proliferation without affecting mitochondrial parameters. All other combinations exhibited more pronounced adverse effects on mitochondrial endpoints. Toxic effects on mitochondrial parameters were observed in all combinations with ddI, d4T, AZT or CBV. TFV and 3TC both attenuated ddI-related cytotoxicity, but worsened the effects of CBV and AZT. CONCLUSIONS The data demonstrate unpredicted interactions between NRTIs with respect to toxicological endpoints and provide an argument against the liberal use of NRTI cocktails without first obtaining data from clinical trials.