Purpose Gender differences in colorectal cancer (CRC) incidence have been previously reported. We designed this population-based study to determine if this gender difference was restricted to specific patient subgroups. Methods Using the Taiwan Cancer Registry database, we identified a total of 124,314 CRCs registered from 1988 to 2007. We compared the incidence of CRCs by gender in all CRCs, in colon and rectal cancers considered separately, and in right-sided versus left-sided colon cancers. Results In individuals aged 50 years and older, the incidence of CRCs was lower in females compared with males. For right-sided colon cancers, the incidence in both genders was similar. Because the proportion of right-sided colon cancer accounted for only one fourth of the total CRCs, its influence on the incidence of total CRCs is reduced. Conclusions Although the incidence of total CRCs is male dominant, the actual gender difference in CRC incidence in Taiwan is limited to the left side of the colon.