The rate of breast cancer screening for women of all ages in Japan is increasing. However, little is known about the biological differences between screen- and self-detected tumors. We used data from the Japanese Breast Cancer Registry (JBCR), a nationwide registry of newly diagnosed breast cancer cases in Japan, to investigate patients diagnosed between January 1, 2004 and December 31, 2011. We compared the clinicopathological features of tumors and assessed yearly trends regarding the proportion of screen-detected cases during the study period. We found that 31.8 % (65,358/205,544) of cancers were detected by screening. Asymptomatic tumors detected by screening (asymptomatic) were more likely to have favorable prognostic features than those that were self-detected (ductal carcinoma in situ [DCIS]: 19.8 versus 4.1 %, node-negative: 77.0 versus 61.6 %, and estrogen receptor-positive [ER+]: 82.0 versus 72.9 %, respectively). All these findings were statistically significant (p < .001). The proportion of breast cancers detected by screening among all cases increased from 21.7 % in 2004 to 37.1 % in 2011. During the same time period, the proportion of screen-detected DCIS increased from 41.5 to 66.0 % and that of ER+ cancers increased from 23.2 to 39.7 %. This study demonstrated that low-risk tumors, including DCIS, ER+, and lower TNM stage, account for a substantial proportion of clinical screening-detected cancers. The differences in biological characteristics between screen- and self-detected cancers may account in part for the limited efficacy of breast cancer screening programs aimed at improving breast cancer mortality.