Colorectal cancer (CRC) is the second most common cancer in Slovenia. The 5-year survival of patients depends on the clinical stage at presentation. More than 70% of patients with CRC are diagnosed as being in stage III or IV, with a 5-year survival rate of 52.7%. To improve the detection rate of CRC and to detect CRC in its early and more curable stage, a national screening programme is needed. In the year 2008, we started a pilot phase of the National CRC screening programme. We invited 9091 Slovene residents aged 64–68 years from Ljubljana, Kranj, and Celje regions, of whom 3807 responded to our invitation (41.9%). Two kits of the faecal immune test were sent to 3117 participants who met the inclusion criteria, and 2829 (90.7%) tests were returned. The compliance rate in our pilot programme was 32.9%. Among the patients who responded positively, 7.5% were positive. Until February 2009, 193 colonoscopies had been performed at DC Bled, DC Lipa and AM DC Rogaška. Intubation to the caecum was carried out in 99.4% of colonoscopies. Histology specimens were taken from 135 patients (70%). The adenoma detection rate was 53.8% (59.8% for men and 47.9% for women; P<0.05). We detected 1–17 adenomas per patient (2.4 on average). Advanced adenomas were detected in 60 patients (31%; 35.1% of men and 27.1% of women; P<0.05). Invasive carcinoma was detected in 15 patients (7.7%; 12.4% of men and 3.1% of women; P<0.05). Ten of them (73.3%) were in clinical stage I or II. In the pilot phase of the CRC screening programme the majority of CRCs were detected at early clinical stages. Invasive cancers were detected in 7.7% of patients. In almost all patients adenomas were resected at screening colonoscopy, thus reducing the possibility of later development of CRC in those patients.