High-resolution recombination rates have recently been revealed in the human genome, and considerable variation in patterns of recombination rates has been found along the chromosomes. Although the associations between this variation and genomic sequence features, such as genic regions, provide information on haplotype diversity and natural selection in these regions, the associations are not well understood. Here, we performed microarray experiments to identify genes specifically expressed in human tissues and investigated tendencies of recombination rates within tissue-specific genes. We found that some types of tissue-specific genes (in the frontal lobe, fetal brain, testis, thymus and thyroid) tended to have extremely low recombination rates, whereas other types (in the brain cerebellum, brain whole, stomach, lung and bone marrow) tended to have relatively high recombination rates. Surprisingly, genes specifically expressed in the frontal lobe, which is a brain region involved in human cognitive abilities, had low recombination rates, whereas genes specifically expressed in the cerebellum, which is a brain region with primitive functions shared by all vertebrate species, had high rates. These findings suggest that natural selection forms the recombination rate tendencies according to the physiological functions exerted in the tissues. For example, the low recombination rates in frontal lobe-specific genes may indicate that a few haplotypes have been rapidly widespread across the population because higher cognitive abilities are advantageous. Frontal lobe-specific genes with extremely low recombination rates may be candidates for genes related to cognitive abilities that human species have recently obtained.