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Objective Inflammatory bowel disease (IBD) and the low prevalence of colorectal cancer (CRC) in younger adults distort the function of the faecal immunochemical test (FIT) for haemoglobin. The National Institute for Health and Care Excellence (NICE) DG 56 recommends additional research on the diagnostic accuracy of FIT in this group of people. An alternative NICE guideline (DG11) exists for the use of another faecal biomarker, calprotectin (FC), to support the early diagnosis of IBD.Design To undertake a primary care, prospective pilot study to evaluate the effect of combining FIT with an established FC pathway (the York Faecal Calprotectin Care Pathway (YFCCP)) on (i) CRC and IBD diagnostic accuracy and (ii) the discriminatory appropriateness of onward referral into either a suspected CRC or a suspected IBD pathway.Results 896 patients were recruited, median age 35 years and 94% fulfilled NICE DG56 criteria. Only one out of 113 FIT+ve patients had CRC, while 36 patients were diagnosed with IBD. FIT had a NPV and PPV for the composite CRC or IBD endpoint of 99% and 27%, respectively, but missed 44% of Crohn’s disease diagnoses. The combination of the YFCCP with FIT resulted in the diagnosis of all patients with CRC and IBD and identified the appropriate discriminatory referral pathways in that patient with CRC and 94% of those with IBD.Conclusion The combination of FIT and FC in the young may allow discriminatory guidance for referral to be developed for the future, for the benefit of patients.