Objective: The Dutch Cleft Palate Association (DCPA) registers all patients with cleft lip or palate and associated congenital anomalies in the Netherlands. The aim of this study was to assess if early registration of cleft patients leads to underreporting of associated congenital anomalies and, if so, whether reregistration is necessary. Methods: The DCPA registration of the birth cohort 1997 to 2001 was compared with the medical files of these cleft patients for prevalence, type, and moment of registration of associated congenital anomalies. To assess possible long-term underregistration, a second birth cohort of 1990 to 1991 was analyzed. Results: The percentage of cleft patients with associated congenital anomalies was 26% in the DCPA database and 33% in the retrospective medical file review. A syndrome, sequence, or association was recognized in 8% of the cleft patients by the DCPA compared with 13% in our medical file review. Of all associated congenital anomalies diagnosed during a follow-up of 12 years, 53% were diagnosed in the first year of life. The cumulative percentage was 59% after 2 years, 62% after 3 years, 80% after 6 years, and 97% after 10 years. Conclusion: Early registration of cleft patients leads to underreporting of other associated anomalies. For a complete registration of associated congenital anomalies in cleft patients, reregistration at a later age is necessary.