BACKGROUND: Although screening for congenital heart malformations is part of the child health care programme in several countries, there are very few published evaluations of these activities. This report is concerned with the evaluation of this screening at the Dutch Child Health Centres (CHC). METHODS: All consecutive patients, aged between 32 days and 4 years, presented at the Sophia Children's Hospital Rotterdam throughout a period of 2 years, with a congenital heart malformation were included in this study. Paediatric cardiologists established whether or not these patients were diagnosed after haemodynamic complications had already developed (diagnosed 'too late'). Parents and CHC-physicians were interviewed in order to establish the screening and detection history. Test properties were established for all patients with a congenital heart malformation (n = 290), intended effects of screening were established in patients with clinically significant malformations (n = 82). RESULTS: The sensitivity of the actual screening programme was 0.57 (95% CI : 0.51-0.62), the specificity 0.985 (95% CI : 0.981-0.990) and the predictive value of a positive test result 0.13 (95% CI: 0.10-0.19). Sensitivity in a subpopulation of patients adequately screened was 0.89 (95% CI: 0.74-0.96). Adequately screened patients were less likely to be diagnosed 'too late' than inadequately screened patients (odds ratio [OR] = 0.20, 95% CI: 0.04-1.05). The actual risk of being diagnosed 'too late' in the study-population (48%) was only slightly less than the estimated risk for patients not exposed to CHC-screening (58%, 95% CI: 43%-72%). Adequately screened patients however were at considerably less risk (17%, 95% CI: 4%-48%). CONCLUSION: Screening for congenital heart malformations in CHC contributes to the timely detection of these disorders. The actual yield, however, is far from optimal, and the screening programme should be improved.