The Norwegian government has funded a pilot study of a national colorectal cancer screening programme. This implies initiation of a screening pilot in the catchment area for two hospitals in Norway. The target population is average risk men and women at age 50-74 years. The programme is designed as a comparative effectiveness programme evaluating acceptance and test performance for two screening methods - fecal occult blood testing (FOBT) and flexible sigmoidoscopy (FS). This protocol describes the main methodological issues, necessary resources and the expected effects.