Introduction: The widespread use of antiretroviral therapy (ART) increased the transmission of antiretroviral resistant HIV strains. ART initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance (TDR) may jeopardize the early goals of early ART among acute/recent HIV infected patients. Methods: Patients with acute/recent HIV infection who underwent resistance test before ART initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. TDR was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without TDR was made using Kruskal–Wallis and Chi-square tests. Results: Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall TDR prevalence was 16.3% (95% confidence interval [CI]: 8.1–30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1–24.5) was against nonnucleoside reverse transcriptase inhibitors (NNRTI), and K103N was the most frequently identified mutation. Conclusions: The high prevalence of NNRTI resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line ART regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for ART naive individuals. Further studies on TDR among acutely/recently HIV-infected are needed to inform on predictors of TDR and ART outcomes among these population.