Spontaneous mutation in RNA viruses is a major determinant of genetic diversity; however, knowledge of HIV-1 mutation rates has largely been limited to cell culture and in vitro studies. Cuevas et al. quantified the HIV-1 spontaneous mutation rate in vivo, based on the frequency of premature stop codons in HIV-1-derived cDNA in peripheral blood mononuclear cells (PBMCs) from infected human patients. The mutation rate in PBMCs was 2 orders of magnitude greater than that predicted by in vitro studies and 44 times higher than in plasma samples, suggesting that most viruses are lethally mutated within PBMCs and fail to reach the plasma. Further analysis revealed that 98% of mutations could be attributed to host editing by A3 cytidine deaminases. The HIV-1 mutation rate was lower in patients with rapidly progressing disease than in those with normal disease, highlighting the antiviral effect of hypermutation by A3. However, variation in the degree of A3-mediated editing suggested that, at low levels, A3 activity may enhance the genetic diversity and pathogenicity of HIV-1.