The aim of the study was to describe the pattern of resistance mutations in human immunodeficiency virus type 1 (HIV-1) infected patients experiencing their first protease inhibitor (PI) failure on nelfinavir (NFV)-containing therapy. Earlier PI-naïve patients (n=172) with NFV-containing therapy were therefore retrospectively studied. Plasma HIV RNA from 43 failing patients was sequenced. In addition, virus from the baseline was sequenced in 29 patients. Failure was defined as two consecutive measurements of viral load of >50 copies/ml after 6 months treatment. Subtyping was done in most patients (n=118). At baseline, the V82A mutation was found in four PI-naïve patients of whom two failed therapy exhibiting this mutation. At therapy failure, 17 of the 43 (40%) patients had primary PI mutations. In nine subjects, RTI-mutations only were found and 17 patients had a wild-type virus. Patients with primary PI and/or RTI mutations had a higher viral load at failure than those who failed with wild-type virus. A surprisingly diverse pattern of primary PI mutations was seen: M46I (n=7), D30N (n=6), L90M (n=5), and V82A (n=4). Four patients exhibited more than one primary PI mutation. PI-naïve patients in Sweden may harbor PI-resistant virus and resistance testing should be considered before treatment. Patients who fail NFV may develop the M46I mutation, which has been related earlier to mainly other PI. The diverse pattern of the evolved PI-mutations and the relative low occurrence of the D30N mutation in the material was unexpected and did not seem to be related to the viral subtype.