Background: One-in-ten Sri Lankans are employed abroad as International Labor Migrants (ILM), mainly as domestic maids or low-skilled laborers. Little is known about the impact their migration has on the health status of the children they ‘leave behind’. This national study explored associations between the health status of ‘left-behind’ children of ILM’s with those from comparative non-migrant families. Methods: A cross-sectional study design with multi-stage random sampling was used to survey a total of 820 children matched for both age and sex. Socio-demographic and health status data were derived using standardized pre-validated instruments. Univariate and multivariate analyses were used to estimate the differences in mental health outcomes between children of migrant vs. non-migrant families. Results: Two in every five left-behind children were shown to have mental disorders [95% CI: 37.4-49.2, p < 0.05], suggesting that socio-emotional maladjustment and behavioural problems may occur in absence of a parent in left-behind children. Male left-behind children were more vulnerable to psychopathology. In the adjusted analyses, significant associations between child psychopathological outcomes, child gender and parent's mental health status were observed. Over a quarter (30%) of the left-behind children aged 6-59 months were 'underweight or severely underweight' compared to 17.7% of non-migrant children. Conclusions: Findings provide evidence on health consequences for children of migrant worker families in a country experiencing heavy out-migration of labour, where remittances from ILM's remain as the single highest contributor to the economy. These findings may be relevant for other labour 'sending countries' in Asia relying on contractual labor migration for economic gain. Further studies are needed to assess longitudinal health impacts on the children left-behind.