Objectives: Examine factors associated with use of traditional medicine during childbirth and in management of childhood diarrhoea. Design: Cross-sectional cluster survey, household interviews in a stratified last stage random sample of 90 census enumeration areas; unstructured interviews with traditional doctors. Setting: Oil-rich Cross River State in south-eastern Nigeria has 3.5 million residents, most of whom depend on a subsistence agriculture economy. Participants: 8089 women aged 15-49 years in 7685 households reported on the health of 11 305 children aged 0-36 months in July-August 2011. Primary and secondary outcome measures: Traditional medicine used at childbirth and for management of childhood diarrhoea; covariates included access to Western medicine and education, economic conditions, engagement with the modern state and family relations. Cluster-adjusted analysis relied on the Mantel-Haenszel procedure and Mantel extension. Results: 24.1% (1371/5686) of women reported using traditional medicine at childbirth; these women had less education, accessed antenatal care less, experienced more family violence and were less likely to have birth certificates for their children. 11.3% (615/ 5425) of young children with diarrhoea were taken to traditional medical practitioners; these children were less likely to receive BCG, to have birth certificates, to live in households with a more educated head, or to use fuel other than charcoal for cooking. Education showed a gradient with decreasing use of traditional medicine for childbirth (χ2 135.2) and for childhood diarrhoea (χ2 77.2). Conclusions: Use of traditional medicine is associated with several factors related to cultural transition and to health status, with formal education playing a prominent role. Any assessment of the effectiveness of traditional medicine should anticipate confounding by these factors, which are widely recognised to affect health in their own right.