Introduction: Chronic kidney disease in one of the significant chronic conditions in human immunodeficiency virus (HIV)-infected population. The nephrotoxicity of antiretroviral therapy, particularly tenofovir disoproxil fumarate, is the important cause of kidney function impairment. There is a need to find reliable markers of early kidney damage. The aim of the study was to evaluate utility of urinary cystatin C levels as a marker of early kidney tubular damage in HIV-1-infected patients. Material and methods: A total of 119 HIV-1-infected patients (88 males, 74.0%) both on antiretroviral therapy (98 individuals, 82.4%) and treatment-naïve, without known kidney disease, and 31 healthy volunteers were enrolled. Cystatin C levels in urine were measured and urine cystatin C/creatinine ratio (UCCR) was calculated. Results: Significantly higher levels of urinary cystatin C were observed in HIV-1-infected group and subgroup on antiretroviral therapy with current CD4+ count below 500 cells/μl (p = 0.008 and p = 0.005, respectively). In patients with albuminuria, both urinary cystatin C and UCCR were significantly higher (p = 0.0035 and p < 0.001, respectively). HIV-1 infection, detectable HIV RNA, low CD4+ nadir, antiretroviral treatment or its length, use of tenofovir, or protease inhibitors had no influence on urinary cystatin C and UCCR. Conclusions: Low current CD4+ cell count was the only HIV-1-related factor influencing urinary cystatin C level. Use of tenofovir or other potentially nephrotoxic antiretroviral drugs did not have any impact on urinary cystatin C levels. Albuminuria was related to higher levels of urinary cystatin C but the background and relevance of this finding is unclear. Utility of urinary cystatin C assessment requires further research in large populations.