Drastic improvement of antiretroviral therapy transformed HIV infection in a manageable chronic condition. However, treatment is strongly compromised with the development of drug resistance mutations, which can be transmitted among treatment naïve individuals as transmitted drug resistance (TDR). Based on the overall prevalence of TDR, European guidelines recommend resistance testing in newly diagnosed individuals prior to treatment initiation. The aim of our study was to determine the prevalence of TDR among newly diagnosed HIV-positive individuals in Slovenia in the years 2017 and 2018. We included 57 plasma samples; we extracted nucleic acids, amplified and sequenced partial protease and reverse transcriptase and/or integrase region of the HIV pol gene. Obtained sequences were analyzed for the presence of TDR mutations. Surveillance drug resistance mutation was found in one patient only (K219Q), corresponding to a prevalence of 1.8% TDR to nucleoside reverse transcriptase inhibitors as well as the overall TDR prevalence. Surveillance mutations conferring resistance to protease and non-nucleoside reverse transcriptase inhibitors were not detected. In addition, no major drug resistance mutations were found in the integrase region. Phylogenetic analysis revealed 22 Slovenian phylogenetic clusters with no observed transmission of TDR. Low prevalence of TDR indicates that no modification is necessary in the national strategy for resistance testing in newly diagnosed treatment naïve HIV-positive individuals; however, continuing surveillance of TDR is still needed.