BACKGROUND: We compare the mental health status of children who reside in Lithuania with parents who are either Lithuanian nationals or non-Lithuanian nationals. METHOD: Data were drawn from the School Child Mental Health Europe survey (SCMHE), a cross-sectional survey of school children aged 6-11years. A total of 1152 Lithuanian children participated, among them 11.7% from a non-Lithuanian family. Child mental health was assessed using the Dominique Interactive (DI) and the parent- and teacher Strength and Difficulties Questionnaire (SDQ). Parental attitudes were evaluated, and socio-demographics were collected. RESULTS: Overall 26.7% of non-Lithuanian versus 17.2% of Lithuanian children reported having an internalizing disorder (p=0.01) mainly due to separation anxiety (16.4% versus 10.2%, p=0.04). Odds ratio (OR) for child-reported internalizing disorders was 1.86 (95% CI=1.17-2.96) once adjusted for other factors including being a girl, to be younger, parental unemployment and low caring and low autonomy parental attitudes which were associated with greater odds of internalizing disorders. In addition, 31.9% of non-Lithuanian reported suicidal thoughts versus 22.0% of Lithuanian children p=.02); OR=1.60 (95% CI=1.04-2.46) once adjusted for single parent, parental unemployment, parental alcohol problems and overreactivity attitude. CONCLUSIONS: Being a non-national minority in Lithuania is a risk factor for child mental health. These findings suggest that further studies are needed to inform local policy-makers on targeted prevention and intervention programs in these children.