Background: High levels of acquired drug resistance have been reported in Cuban HIV-1 infected patients. The aim of this study is to determine the levels of primary HIV drug resistance in newly diagnosed Cuban´s patients. Material and methods: Demographic, clinical and laboratory data were collected from 225 newly diagnosed HIV-1 patients from Cuba between April 2013 and April 2014. Sequences of 187 patients were analyzed. The HIV-1 pol gene was sequenced using Sanger sequencing. Drug resistance was interpreted according to the WHO surveillance drug-resistance mutations list, 2009. HIV-1 subtyping was performed using the Rega subtyping tool version 3. Results: The mean age at sampling time was 33.5 years, 80.7% of the patients were men and the major transmission route was MSM (80.1%). The 27.2% of patients had HIV-1 chronic infection and 72.7% recent infection. The median viral load value was 60,300 RNA copies/mL (16,900 - 133,000), and median CD4+ count value was 359 cells/mm3 (263-558). In the 17.6% (33/187), of the studied viruses, transmitted resistance mutations were detected. Simple nonnucleoside mutants were the most common (1.1%), followed by double class resistance against to nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors (8.0%) and single mutants to the protease inhibitors (2.1%). From the 33 patients with transmitted drug resistances mutations, 22 (66.6%) were MSM, 26 (78.8%), were diagnosed with a recent HIV-1 infection, 13 (39.4%) were from Havana Conclusions: This study highlights the need of further studies in order to elucidate the factors that influencing the high levels of resistance in newly diagnosed population, in order to take actions toward the possible causes. It also reinforces the need for drug resistance testing in patients that start therapy. It was shown that first-line therapy may not be effective, so in 2016 it is replaced by Atripla.