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Antiretroviral therapy (ART) may negatively affect renal function through drug toxicity mechanisms [1] or improve renal function by ameliorating the detrimental effects of untreated human immunodeficiency virus (HIV) on the kidney [2, 3]. Several studies have suggested that use of tenofovir disoproxil fumarate is associated with worse changes in estimated glomerular filtration rate (eGFR) compared with other nucleoside reverse-transcriptase inhibitors (NRTIs), and that this effect is magnified with concomitant use of protease inhibitors (PIs) [4–8]. However, not all studies have confirmed this relationship [9–11]. In the AIDS Clinical Trials Group (ACTG) 5202 trial, worse changes in eGFR (estimated as creatinine clearance using the Cockcroft-Gault equation [12]) were found with the use of tenofovir/emtricitabine compared with abacavir/lamivudine, especially when tenofovir/emtricitabine was used in combination with atazanavir/ritonavir [13]. Other observational studies have suggested that the antiretroviral PI combination atazanavir/ritonavir also negatively affects renal function [14, 15]. There is growing interest in the use of serum cystatin C as a new marker of renal function. Compared with serum creatinine, cystatin C is not affected by muscle mass and is completely eliminated by the kidney through glomerular filtration. Perhaps because of this improved ability to measure glomerular filtration, cystatin C seems to have greater utility over creatinine in predicting adverse outcomes in both the general population [16–18] and in the HIV-infected population [19, 20]. As such, newer GFR-estimating equations have been developed using cystatin C, including the 2012 Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) cystatin C equation, which uses cystatin C only without creatinine, and the 2012 CKD-EPI cystatin C-creatinine equation, which incorporates both markers [21]. In the general US population [18], identifying renal dysfunction with the 2012 CKD-EPI cystatin C-creatinine combined equation appears to be more predictive of cardiovascular disease, end stage renal disease, and overall mortality compared with the 2012 CKD-EPI cystatin C equation and the older 2009 CKD-EPI equation [22], the latter of which includes only serum creatinine. A recent study in women infected with HIV suggested that both of the newer 2012 cystatin C-based equations were more accurate than the 2009 CKD-EPI equation in identifying those patients with renal dysfunction with greater risk of mortality [20]. A recent American study using iohexol clearance as the reference measurement of GFR assessed the accuracy of these newer cystatin C-based equations in patients infected with HIV, most of whom were receiving antiretroviral medications, and found that that the 2012 CKD-EPI cystatin C-creatinine combined equation most accurately estimated GFR compared with the 2012 CKD-EPI cystatin C equation and the original 2009 CKD-EPI equation [23]. Another American study corroborated these findings by again finding that the 2012 CKD-EPI cystatin C-creatinine combined equation was more accurate than the other 2 CKD-EPI equations when compared with direct GFR measurement using iohexol clearance [24]. However, in a similar study conducted in Europe, no appreciable differences were found between the combined 2012 CKD-EPI equation and the 2009 CKD-EPI equation [25]. Of note, both of these HIV studies suggest that all 3 CKD-EPI equations were significantly more accurate than the Modification of Diet in Renal Disease (MDRD) equation [22], which is important given that much of our understanding of the effects of antiretrovirals on renal function from observational cohort studies used this latter equation [7, 26]. Therefore, we assessed changes in renal function using 5 different estimating equations in ACTG 5224s, a substudy of ACTG 5202, in which cystatin C was systematically measured, and assessed the nephrotoxicity profiles with commonly used once-daily regimens.