The hypothesis that filgrastim (r-met-huG-CSF) activates replication of minor variants of human inmmunodeficiency virus type 1 (HIV-1) was tested by analysis of plasma quasi-species composition in 7 subjects in whom plasma HIV-1 RNA had increased during filgrastim treatment. Inferred phylogenetic trees of env sequences from 3 subjects during filgrastim treatment contained unique intrasubject subclusters that shared a most recent common ancestor with the baseline HIV-1 quasi species. Genotypes in the unique subclusters were not detected before filgrastim treatment, yet they composed 40%-70% of the plasma quasi species during treatment. The minority variants that appeared in 1 subject were more distantly related to plasma quasi species present 5 years before filgrastim treatment than were the majority of the pretreatment plasma quasi species. These findings provide evidence that increased HIV-1 replication during filgrastim treatment was associated with activation of HIV-1 variants that, before filgrastim treatment, were minor components of the plasma quasi species.