The main goal of this experiment was to analyze mutations associated with resistance of HIV type 1 to antiretroviral drugs (integrase inhibitors, reverse transcriptase inhibitors and protease inhibitors) in treatment-naïve patients and compare them with mutations in treatment-experienced patients having virologic failure, and also compare interpretation of biological significance of these detected mutations with three bioinformatic algorithms. Resistance of HIV to antiretroviral drugs was detected by” populations-based” sequencing method of pol region of the HIV genome. Major mutations associated with HIV resistance to antiretroviral drugs were detected in 2/20 (10%) treatment naïve and in 6/20 (30%) patients having treatment failure. Major mutations associated with resistance to integrase inhibitors (N155H and Q148R) leading to cross-resistance between raltegravir and elvitegravir were detected in two treatment experienced patients. Resistance to nucleoside inhibitors of reverse transcriptase was detected in 4/11 (36,4%) treatment experienced patients and in 2/19 (10,5%) treatment naïve patients. Major mutations to protease inhibitors were not detected, while mutation G140A that causes HIV resistance to non- nucleoside inhibitors of reverse transcriptase was detected in one treatment experienced patient. The most common major mutation detected in this experiment was M148V/I that causes resistance to nucleoside reverse transcriptase inhibitors. 85% of all patients were infected with HIV-1 subtype B. The results of this experiment are the first one in Croatia referring to HIV resistance to integrase inhibitors. Mutations associated with HIV resistance to antiretroviral drugs in treatment naïve and experienced patients are different, and there are also nonconformities with interpretation of their biological significance depending on different bioinformatics algorithms.