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Tenofovir is associated with reduced renal function, but it is not clear whether there is a greater decline in renal function when tenofovir is co-administered with a boosted protease inhibitor rather than with a nonnucleoside reverse transcriptase inhibitor (NNRTI).We calculated the estimated glomerular filtration rate (eGFR) for patients in the Swiss HIV Cohort Study. We estimated the difference in eGFR over time between first therapies containing tenofovir and either the NNRTI efavirenz or the protease inhibitors lopinavir (LPV/r) or atazanavir (ATV/r), both boosted with ritonavir.Patients on a first therapy of tenofovir co-administered with efavirenz (n = 484), LPV/r (n = 269) and ATV/r (n = 187) were followed for a median of 1.7, 1.2 and 1.3 years, respectively. Relative to tenofovir and efavirenz, the estimated difference in eGFR for tenofovir and LPV/r was −2.6 ml/min per 1.73 m2 [95% confidence interval (CI) −7.3 to 2.2) during the first 6 months of therapy, then followed by a difference of 0.0 ml/min per 1.73 m2 (95% CI −1.1 to 1.1) for each additional 6 months of therapy. Relative to tenofovir and efavirenz, the estimated difference in eGFR for tenofovir and ATV/r was −7.6 ml/min per 1.73 m2 (95% CI −11.8 to −3.4) during the first 6 months of therapy, then followed by a difference of −0.5 ml/min per 1.73 m2 (95% CI −1.6 to 0.7) for each additional 6 months of therapy.Tenofovir with either boosted protease inhibitor leads to a greater initial decline in eGFR than tenofovir with efavirenz; this decline may be worse with ATV/r than with LPV/r.