The study assessed inequalities in mortality of Lithuanian urban and rural populations throughout the period of socio-economic transition (1990-2000). Mortality from major causes of death, except cancers in females, was higher among the rural population. Inequality in mortality increased during the period of transition, especially among males, mainly due to more rapidly improving health of the urban population. Cardiovascular diseases and external causes made the largest contribution to the inequality. Differences in mortality of urban and rural populations point to greater social and psychological stress affecting the rural population, unhealthy life styles, inequities in accessibility of health care and lack of preventive programs in rural areas.