There are several candidate screening modalities - fecal occult blood (FOBT), flexible sigmoidoscopy, colonoscopy, CT and MRI colonography and a range of molecular markers. Of these, only FOBT and FS have been subjected to long-term follow-up in randomised trials (RCTs). These two modalities will be tested in a head-to-head comparison by 1:1 randomisation. Previous studies have suggested that the attendance for FS may be lower than for FOBT. However, participation has been shown to decline with repetitive rounds required for FOBT, while infrequent or once-only screening may suffice for FS. A better test performance for FS makes it uncertain which method may be most beneficial in a public health perspective. This is the first time a national screening programme is designed as a platform for comparative effectiveness studies.