Objective To assess the role of rural–urban migration in the risks of under-five death; to identify possible mechanisms through which migration may influence mortality; and to determine individual- and community-level relationships between migration status and under-five death.

Method Multilevel Cox regression analysis was used on a nationally representative sample of 6029 children from 2735 mothers aged 15–49 years and nested within 365 communities from the 2003 Nigeria Demographic and Health Survey. Hazard ratios with 95% confidence intervals were used to express the measures of association between the characteristics, and intra-class coefficients were used to express the measures of variation.

Results Children of rural non-migrant mothers had significantly lower risks of under-five death than children of rural–urban migrant mothers. The disruption of family and community ties, low socio-economic position and vulnerability, and the difficulties migrants face in adapting into the new urban environment, may predispose the children of rural–urban migrants to higher mortality.

Conclusion Our results stress the need for community-level and socio-economic interventions targeted at migrant groups within urban areas to improve their access to health care services, maternal education, as well as the general socio-economic situation of women.