The aim of this study was to compare and get a deeper insight into issues of the health and health behavior inequalities among Lithuanian, Polish and Russian school-aged children in national and international contexts. Investigations were carried out in the framework of Health Behavior in School-aged Children (HBSC) study - a WHO collaborative cross-national survey. Five thousand seven hundred and seventy six randomly selected students aged 11, 13, and 15 years of age answered questionnaires in the classroom in 108 schools located in different regions in Lithuania in March–April of 2006. Questions on perceived health and health related behaviors were addressed to the respondent (response rate was 95 %). 5632 questionnaires were selected for further analysis by the international data center in Bergen. SPSS version 11.5 and multilevel analysis program MLwiN 2.0 was applied for statistical analysis of data. Relatively minor inequalities in health and health behavior were established when comparing different health and health behavior indicators in Lithuanian, Polish and Russian school-aged children in Lithuania. These disparities are lower in comparison with differences, which were established among respondents of HBSC international studies. Odds ratios to have negative self-rated health evaluation were higher in girls of Russian (OR-1.71, p<0.05) and Polish (OR-1.62, p<0.05) nationality. Therefore, Russian and Polish students were tending to have higher odds ratios for perception of happiness (p<0.05). Respondents of Russian nationality have expressed less somatic and psychological complaints. Polish boys (OR=1.38, p<0.05) were tending for higher prevalence of headache, but have expressed fewer complaints for depression (OR=0.65, p<0.05), anxiety (OR=0.71, p<0.05). Chances to be involved in risk taking behaviors (alcohol consumption, smoking, drug use) were lower among Polish and Russian respondents. In schools with Lithuanian language based-schoold, health and health behavior indicators were more negative in Polish and Russian respondents in comparisons with their Lithuanian peers However, Lithuanian students, who were enrolled in Russian and Polish schools, tending to have better perceived health evaluation and better health behavior in comparison with their peers of Polish and Russian nationality. Analysis shows, that Polish and Russian students are integrated well into Lithuanian society and being a member of the minority class is not related to poor health or negative lifestyle. Therefore, with few exceptions universal health promotion programs should be provided to school-aged children of all ethnicities and cultural backgrounds.