Objective We have compared the performance of two faecal immunochemical tests (FIT) in an average-risk population. Materials and methods Altogether, 10 000 individuals aged 50-74 were selected randomly from the population of Latvia in 2011 and assigned randomly either to OC-Sensor or to FOB Gold single-time testing. Positivity of the test, frequency of colonic lesions, number needed to screen (NNscreen) and scope for the detection of an advanced neoplasm (cancer and advanced adenoma) were compared between the tests using the same cutoff concentrations in μg/g faeces. Confidence intervals (CIs) at 95% were calculated. Results Positivity with the cutoff set at 10 μg/g faeces was 12.8% (95% CI: 11.4-14.2) for FOB Gold and 8.3% (95% CI: 7.2-9.4) for OC-Sensor (P<0.001). Positivity was higher in men and the older age groups. Colonoscopy compliance was 55.5%. There was no significant difference between the two tests at comparable cutoff concentrations in μg/g, colonoscopy attendance rate or colonoscopy results. For advanced neoplasm detection, there was no significant difference in number needed to scope and NNscreen at a cutoff of 10 μg/g faeces; however, lower NNscreen was required to detect advanced neoplasms with the FOB Gold test at increased cutoff concentrations. Conclusion Different quantitative FIT systems may report different positivity rate at identical cutoff concentrations, which has to be considered when implementing the use of FIT in national screening programmes.