GC-biased gene conversion (gBGC) is a recently discovered, recombination-associated segregation distortion, which influences GC-content dynamics in the mammalian genome. We scanned the primate proteome for examples of exon-specific, lineage-specific accelerated amino acid evolution. Here, we show that such episodes are frequently accompanied by an increase in GC-content, which extends to synonymous and intronic positions. This demonstrates that gBGC has substantially (negatively) impacted the evolutionary trajectory of human proteins by promoting the fixation of deleterious AT-->GC mutations.