Introduction: The incidence of colorectal cancer in the Czech Republic is continuously increasing. A national screening programme based on the biennial FOBT and colonoscopy, in the event of FOBT positivity, was launched in 2000. The total number of colonoscopies increased by 50%, reaching approximately 130,000 (3.5% of the eligible population) per year. The number of FOBT has multiplied. The aim of this prospective multicenter study was to assess the potential role of colonoscopy in the diagnosis and screening of colorectal cancer in the conditions of the screening programme. Results: A total of 3827 colonoscopic records were analyzed. The mean rate of caecum intubation was 87.6%. The most frequent indication for colonoscopy was enterorrhage (32.4%) followed by pain (27.5%) and changes in stool habits (21.3%). Overall, 542 (14.1%) colonoscopies were performed as an official screening method following either positive (395) or negative (147) FOBT. A total of 385 (10.1%) colonoscopies were performed as a primary screening procedure without previous FOBT (altogether 927 - 24.2% - screening procedures). 2251 polyps in 1172 patients (30.5%), 334 advanced adenomas in 269 patients (7,0%), and 143 (3.7%) carcinomas were found. In 479 patients reporting a positive family history, carcinoma was detected in 7 (1.5%) and advanced adenoma in 19 (4.0%) of them, which was lower than in 3348 patients without a positive family history (136 cancers: 4.1%, 315 advanced adenomas: 9.4%), but 212 procedures were done as part of the screening (44.2% vs. 21.3% in patients without positive family history). Among 1395 patients reporting blood in the stool, 141 patients underwent FOBT (106 positive, 35 negative). In patients with enterorrhage, carcinomas were found in 75 (5.4%) patients, which is higher than their occurrence in 2432 other patients (69 cancers: 2.8%). Altogether, ninety four (37.1%) of advanced adenomas and 51 (36.7%) carcinomas were detected by screening. Conclusions: We proved yield of the screening programme based on FOBT and colonoscopy, since a relatively high proportion of all colonoscopies was indicated either after FOBT or as primary screening procedures, and a relatively high proportion of advanced lesions was detected by screening. Surprisingly, in patients with a positive family history, the detection rate of significant lesions was rather low, which could be explained by the relatively high rate of screening procedures in this group. The consequences of the screening process have to be analyzed with caution.