Although colorectal cancer (CRC), a major type of cancer worldwide, has shown a proximal or right-sided shift in subsite distribution in western countries, trends in subsite incidence in Asian countries remain unclear. Here, we evaluated subsite-specific trends in CRC incidence rate between 1978 and 2004 in Japan using large data from 10 population-based cancer registries. The colorectal sites (C18–C20) were categorized into three groups: proximal colon (C18.0–C18.5), distal colon (C18.6–C18.7), and rectum (C19.9 and C20.9). Trends in age-standardized incidence rates (ASRs) were characterized by joinpoint regression analysis. A total of 303 802 CRC cases were analyzed. Overall, ASRs increased remarkably until 1993, with an annual percentage change (APC) of 4.9%, and then stabilized thereafter. By subsite, however, ASRs of proximal colon significantly increased, with APCs of 7.1% (1978–1991), 3.8% (1991–1996), and 0.9% (1996–2004); distal colon showed an initial significant increase, with an APC of 7.6%, but stabilized from 1991 until the end of observation; and rectal cancer showed an initial significant increase, with APCs of 1.9% (1978–1988) and 5.6% (1988–1992), but then decreased abruptly in 1992, the year CRC screening was introduced nationwide, with an APC of −1.0%. Thus, we revealed that changes in incidence trends for the three anatomic sites apparently began to differ in the 1990s. Careful monitoring is necessary to confirm whether these trends are changing in the Japanese population.