Objective The first level of a colorectal cancer (CRC) screening process was systematically analysed using the Healthcare Failure Mode and Effects Analysis (HFMEA) approach by a multidisciplinary team aiming to improve the programme quality. Setting The study was conducted at the Local Health Authority of Bologna, Northern Italy. Methods Seven brainstorming sessions were conducted and all the activities performed were recorded on a FMEA worksheet consisting of individual records reporting the specific phases of the analysed process along with associated activities, possible failure modes, their causes and effects, the obtained risk priority numbers (RPNs) and the control measures to plan. Results Twenty-three failure modes, 14 effects and 12 possible causes were identified. Nine failure modes were prioritised according to the RPN obtained; most resulted in possible false-negative faecal immunochemical test (FIT) results (66.7%), followed by sample loss (22.2%) and not reaching the entire target population (11.1%). This leads to 66.7% of corrective/preventive actions being applied to the phase of returning the stool sample by the citizen. For this phase reorganisation, the local pharmacies were involved not only as FIT kit delivery points but also as specimen collection and sending points to the laboratory. These organisational changes allowed the introduction of complete traceability of kits and specimens flow, as well as temperature control. A re-evaluation of the prioritised failure modes 6 months after launching the implemented screening process showed that HFMEA application decreased the risk of potential errors by 75.9%. Conclusion HFMEA application in CRC screening programme is a useful tool to reduce potential errors.