Background: Toxoplasmosis is a common opportunistic infection in AIDS patients. The routine diagnostics is based on serologic testing and IgG avidity index, but it may have limited utility in immunodeficient patients; thus, it is recommendable to detect T. gondii DNA in subjects with advanced HIV disease. The results of the studies published so far focused on patients with clinical symptoms of toxoplasmosis. Our study encompassed a group of HIV-infected subjects on cART therapy, without immunological disturbances and clinical symptoms of T. gondii infection. Methods: The study was retrospective, and samples were collected between 2013 and 2016. We evaluate the prevalence of serological (IgM, IgG, and avidity IgG) and molecular (DNA) T. gondii infection markers in asymptomatic HIV-infected patients and the control group using serologic (ELISA) and quantitative (real-time PCR) molecular testing. Results: Of 152 HIV-infected in routine follow-up tested for T. gondii IgM and IgG, 6 (3.9%) and 50 (32.9%) were positive, respectively. Of 168 serum samples from blood donors, 1 (0.6%) and 49 (29.2%) were IgM+ and IgG+ positive, respectively. IgM seroprevalence in HIV-infected patients was significantly higher than in blood donors. T. gondii DNA (genotype II) was identified in 47 (30.9%) HIV-infected patients, with 13 (8.6%) IgM−IgG− samples. In blood donors, T. gondii DNA was present in 15 (8.9%) IgM−IgG−. Conclusions: In both groups, T. gondii DNA was detectable in seronegative subjects, implying the need to supplement the routine serological testing via the molecular method. It can help the accurate monitoring of the reactivation of infection in asymptomatic HIV-infected persons, and the quick introduction of specific therapy, in blood donors, would be of high importance for safe blood donations.