To examine the nucleotide diversity at silent (synonymous+intron+untranslated) and non-silent (nonsynonymous) sites in chimpanzees and humans, genes at six nuclear loci from two chimpanzees were sequenced. The average silent diversity was 0.19%, which was significantly higher than that in humans (0.05%). This observation suggests a significantly larger effective population size and a higher extent of neutral polymorphism in chimpanzees than in humans. On the other hand, the non-silent nucleotide diversity is similar in both species, resulting in a larger fraction of neutral mutations at non-silent sites in humans than in chimpanzees. Other types of polymorphism data were collected from the literature or databases to examine whether or not they are consistent with the nuclear DNA sequence polymorphism observed here. The nucleotide diversity at both silent and non-silent sites in mitochondrial (mt) DNA genes was compatible with that of the nuclear genes. Microsatellite loci showed a similar high extent of heterozygosity in both species, perhaps due to the combined effect of a high mutation rate and a recent population expansion in humans. At protein loci, humans are more heterozygous than chimpanzees, and the estimated fraction of neutral alleles in humans (0.84) is much larger than that in chimpanzees (0.26). These data show that the neutral fraction in non-silent changes is relatively large in the human population. This difference may be due to a relaxation of the functional constraint against proteins in the human lineage. To evaluate this possibility, it will be necessary to examine nucleotide sequences in relation to the physiological or biochemical properties of proteins.