Background: Immunization coverage is a major health indicator. In Israel, routine childhood immunizations are provided at community public well-baby clinics. Immunization monitoring is an important cornerstone of a national health policy; however data obtained through sampling carries the risk of under-representation of certain population strata, particularly high-risk groups. Despite high national average immunization coverage, specific sub-populations are under-immunized, as highlighted by outbreaks of vaccine-preventable diseases.Methods: Implementation of a national childhood immunization registry.Results: The mean national immunization coverage at age two years (2007 data) was: DTaP-IPV-Hib4 (all 95%), HBV3 (99%), MMR1 (97%), HAV1 (93%). These reports are based on a 17% population-based sample in some districts and on cumulative reports in others. The new national immunization registry requires data completeness, protection of confidentiality, compulsory reporting by providers, and links to other computerized health records. It would provide individual immunization data from infancy to adulthood and be accessible to both providers and consumers. During 2008 the Ministry of Health in Israel launched a national immunization registry based on immunization reporting from well-baby clinics using a web-based computerized system. As of December 2010, 210 well-baby clinics are connected to the nascent registry, which includes the records of some 100,000 children.Conclusions: The comprehensive national immunization registry augurs well for the prospect of evidence-based assessment of the health status of children in Israel.