BACKGROUND: The European literature on mental health of the children of immigrants is limited. Therefore this study aims to investigate gender-specific mental health reported by teachers, parents and the children themselves in 12-year old children of immigrants and non-immigrants and also to study the level of agreement between the different informants. METHODS: This cross-sectional study is a part of the longitudinal South East Sweden Birth Cohort-study (the SESBiC-study) on children’s health. All children born in town in the south of Sweden 1995-1996 were invited to take part. The mothers of 1723 children (88%) consented. In this part 87 Swedish-born 12-year old children of immigrants and 687 12-year old children of non-immigrants were investigated regarding gender-specific differences in mental health as reported by teachers (Teacher-report form), parents (Child behavior checklist), and children (Strengths and Difficulties Questionnaire) and the agreement reached between the informants. RESULTS: Parental immigrant status was not associated with mental health in any of the groups, but living arrangements and parental educational level were mainly found to have an effect on the health status of boys (TRF-Internalizing beta = .77 95% CI = .02-1.52; TRF-Externalizing.beta = 2.31 95% CI = .63-3.99; TRF-Total beta = 6.22 95% CI = 2.27-10.18) The agreement between different informants was generally low, except for externalizing problems among boys (Boys of immigrant parents: Parent and teacher correlation rho = .422 and Child teacher correlation rho = .524, p-value < .05, respectively). The correlation between teachers and parents were lower in the index group compared to the reference group. In the index group, the correlations between teacher's and children's assessments were fairly high for boys but not for girls (rho Total = .400, rho Internalizing = .240 and rho Externalizing = .524, p-value < .05 for Total and Externalizing). CONCLUSION: This study confirms previous findings that the mental health of children of immigrants is similar to that of children of non-immigrants. We found that family factors have a greater impact on the reported mental health than immigrant status does. This might be of clinical importance for healthcare workers to recognize when investigating and treating children from other cultures.