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Background Participation rates in colorectal cancer screening are below recommended European targets. Aim To evaluate the effectiveness of an alert in primary care electronic medical records (EMRs) to increase individuals’ participation in an organised, population-based colorectal cancer screening programme when compared with usual care. Design and setting Cluster randomised controlled trial in primary care centres of Barcelona, Spain. Method Participants were males and females aged 50–69 years, who were invited to the first round of a screening programme based on the faecal immunochemical test (FIT) ( n = 41 042), and their primary care professional. The randomisation unit was the physician cluster ( n = 130) and patients were blinded to the study group. The control group followed usual care as per the colorectal cancer screening programme. In the intervention group, as well as usual care, an alert to health professionals (cluster level) to promote screening was introduced in the individual’s primary care EMR for 1 year. The main outcome was colorectal cancer screening participation at individual participant level. Results In total, 67 physicians and 21 619 patients (intervention group) and 63 physicians and 19 423 patients (control group) were randomised. In the intention-to-treat analysis screening participation was 44.1% and 42.2% respectively (odds ratio 1.08, 95% confidence interval [CI] = 0.97 to 1.20, P = 0.146). However, in the per-protocol analysis screening uptake in the intervention group showed a statistically significant increase, after adjusting for potential confounders (OR, 1.11; 95% CI = 1.02 to 1.22; P = 0.018). Conclusion The use of an alert in an individual’s primary care EMR is associated with a statistically significant increased uptake of an organised, FIT-based colorectal cancer screening programme in patients attending primary care centres.