The influence of religion on health remains a subject of considerable debate both in developed and developing settings. This study examines the connection between the religious affiliation of the mother and under-five mortality in Mozambique. It uses unique retrospective survey data collected in a predominantly Christian area in Mozambique to compare under-five mortality between children of women affiliated to organised religion and children of non-affiliated women. It finds that mother’s affiliation to any religious organisation, as compared to non-affiliation, has a significant positive effect on child survival net of education and other socio-demographic factors. When the effects of affiliation to specific denominational groups is examined, only affiliation to the Catholic or mainline Protestant churches and affiliation to Apostolic churches are significantly associated with improved child survival. It is argued that the advantages of these groups may be achieved through different mechanisms: the favourable effect on child survival of having mothers affiliated to the Catholic or mainline Protestant churches is likely due to these churches’ stronger connections to the health sector, while the beneficial effect of having an Apostolic mother is probably related to strong social ties and mutual support in Apostolic congregations. The findings thus shed light on multiple pathways through which organised religion can affect child health and survival in sub-Saharan Africa and similar developing settings.