The objective was to study the prevalence of genotypic resistance to nucleoside analogues (NRTIs), nonnucleoside analogues (NNRTIs), and protease inhibitors among HIV-1-infected persons in Athens, Greece. Patients followed at two HIV units were examined for prevalence of emergence of antiretroviral resistance mutations (ARMs) in this observational study where complete therapy history was available. All mutations were recorded according to the October/November 2005 IAS-USA Drug Resistance Mutations Figures. A total of 234 patients underwent genotypic testing of 2069 followed (1987-2004). The most frequent ARMs of each drug category were to NRTIs at codons M184V [present in 149 tests (63.6%)], M41L [79 (33.8%)], K70R [66 (28.2%)], M184VI [58 (24.8%)], T215YF [53 (22.7%)], D67N [82 (35.0%)], T215Y [72 (30.8%)], K219Q [47 (20.1%)], K219E/Q [54 (23.1%)], and L210W [49 (20.9%)], respectively. The most prevalent mutations related to NNRTIs were K103N [present in 59 tests (25.2%)], G190A [50 (21.4%)], and Y181C [48 (20.5%]. Mutations in the protease gene showed that the ARM at residue L63P was the most prevalent present in 119 samples (50.9%). L90M (26.5%) was among the most frequently observed single key protease mutations in our series, although variables of V82 and I54 amino acid substitutions were more frequent. M184V (63.6%) and K103N (25.2%) were the most frequent mutations related to NRTIs and NNRTIs, respectively.