Incidental prostate cancer is often found in cystoprostatectomy specimens. The presence of a clinically significant tumour has an impact on follow-up strategies. In prostatectomy specimen for prostate cancer, whole-mount sections improve diagnostic accuracy. The present study compares detection of incidental prostate cancer in complete to routine processing. We included 295 consecutive patients who underwent radical cystoprostatectomy. Between 01/1995 and 12/2003 (period I), specimens of 129 patients were partially processed, whereas between 01/2004 and 03/2009 (period II), specimens of 166 patients were completely processed. Incidental prostate cancer was detected overall in 91 (30.8 %) patients. Prostate cancer was detected in 24 (18.6 %) patients in period 1 and in 67 (40.4 %) patients in period 2 (p < 0.001). Potentially clinically significant prostate cancer was detected in 12 (9.2 %) and 29 (17.5 %) patients, respectively (p = 0.044). Complete embedding and processing of cystoprostatectomy specimen yield significantly more potentially clinically relevant prostate cancers. The present data suggest that notably in younger men the specimens should be completely processed.