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.