BACKGROUND: Numerous child health status measures have been developed, ranging from assessments of physical and mental health to activity continuums. Our objective was to report the regional distribution of physical morbidity among children in Manitoba. METHODS: Using Manitoba's population-based prescription and health care data for 1998/99, the prevalence of children with lower respiratory tract infections, four chronic conditions (asthma, cardiovascular disease, Type 1 diabetes mellitus and seizure disorders) and physical disabilities, including spina bifida and cerebral palsy, was determined for 12 Regional Health Authorities and 12 Winnipeg Community Areas, ranked by a measure of population healthiness, the premature mortality rate (PMR). Prescription rates were also reported by neighbourhood income quintile, derived from census data. RESULTS: Hospitalization for lower respiratory tract infection was highest in infants (6%) and increased with successive decreases in neighbourhood income or in the population healthiness of a region. On the basis of a physician diagnosis or prescription drug for asthma, 10% of school-age children had asthma. Asthma treatment rates in northern Manitoba were substantially lower than in Winnipeg. Treatment rates for cardiovascular conditions, Type I diabetes and seizure disorders approached 1% in adolescents and there were no regional differences in the distribution of these conditions. The prevalence of physical disability was highest in northern Manitoba. CONCLUSION: A minority of Manitoba children suffer from chronic and serious acute health problems in childhood, but the burden of illness is not evenly distributed among children.