Our objective was to investigate regional health differences among Finnish children using a population-based longitudinal register data. All live births born in 1987 were included in the study (N=59,546) and followed-up until the age of seven years. Statistically significant regional variation was found for all health indicators but diabetes. Background variables, such as maternal age and social class, explained only the difference in mortality. Various indicators gave different geographical patterns. Regional equity in childhood health has not been achieved in Finland. Existing health registers were feasible in studying regional variation in health, but a set of comprehensive morbidity indicators - preferably derived from different data sources - should be developed to monitor equity in health.