Recently, a new Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) formula was presented as a better alternative to the modification of diet in renal disease (MDRD) formula for GFR estimation (eGFR) in patients with relatively well-preserved kidney function. The main objective of our study was to compare the eGFR results arrived by the new CKD-EPI to the older MDRD equation in antiretroviral (ARV)-naive and ARV-treated HIV-1-infected patients. The study was performed in 287 adult HIV-1-infected patients and was an evaluation comparing eGFR results based on age, gender, race, and serum creatinine. The biggest difference in estimated glomerular filtration rate (eGFR) measured by the two formulas was seen in ARV-naive men with well-preserved kidney function (p = 0.001). Moreover, we found a significant negative correlation between mean difference in eGFR measured by the two equations and the age of the studied subjects (r = -0.37, p < 0.001). No correlation was observed between mean difference in eGFR and HIV viral load (r = -0.15, p = 0.2). Independent of the equation used, a significant decrease of eGFR in ARV-treated in comparison to ARV-untreated HIV-1-infected patients was seen (p < 0.001). In conclusion, in HIV-1-infected subjects, especially in ARV-naive men with well-preserved kidney function, eGFR measured by MDRD and CKD-EPI formulas varies strongly following the method used. Such discrepancies may be important in everyday clinical practice and must be confirmed by additional studies using GFR measured with a reference method.