The difference in cognitive skills between humans and nonhuman primates is one of the major characters that define our own species. It was previously hypothesized that this divergence might be attributable to genetic differences at gene expression level, and the cis-regulating elements of gene 3'UTRs might play important roles in the post-transcriptional regulation of gene expression. In this study, we constructed a cDNA library from the prefrontal cortex of rhesus monkey and generated a total of 754 high-quality ESTs. Using rhesus macaque as outgroup, we calculated the evolutionary rates of the 3'UTRs of 52 brain-expressed genes in humans and chimpanzees in order to dissect the role of natural selection during primate brain evolution. Comparison of 52 orthologous gene sequences of human and chimpanzee indicated that the mean substitution rates at nonsynonymous sites (K(a)), synonymous sites (K(s)) and 3'UTRs (K(3u)) are 0.0024, 0.0116 and 0.0117, respectively. Relative rate tests and acceleration index tests demonstrated that only a few genes had significant rate divergence between human and chimpanzee. The 3'UTRs of the brain-expressed genes in primates has a similar evolutionary rate with the synonymous sites of the gene coding region, indicating a neutral evolution of the 3'UTR sequences in human.