Objective: To identify the magnitude of anaemia and deficiencies of Fe (ID) and vitamin A (VAD) and their associated factors among rural women and children. Design: Cross-sectional, comprising a household, health and nutrition survey and determination of Hb, biochemical (serum concentrations of ferritin, retinol, C-reactive protein and α 1 -acid glycoprotein) and anthropometric parameters. Multivariate logistic regression examined associations of various factors with anaemia and micronutrient deficiencies. Setting: Kalalé district, northern Benin. Subjects: Mother-child pairs (n 767): non-pregnant women of reproductive age (15-49 years) and children 6-59 months old. Results: In women, the overall prevalence of anaemia, ID, Fe-deficiency anaemia (IDA) and VAD was 47·7, 18·3, 11·3 and 17·7 %, respectively. A similar pattern for anaemia (82·4 %), ID (23·6 %) and IDA (21·2 %) was observed among children, while VAD was greater at 33·6 %. Greater risk of anaemia, ID and VAD was found for low maternal education, maternal farming activity, maternal health status, low food diversity, lack of fruits and vegetables consumption, low protein foods consumption, high infection, anthropometric deficits, large family size, poor sanitary conditions and low socio-economic status. Strong differences were also observed by ethnicity, women's group participation and source of information. Finally, age had a significant effect in children, with those aged 6-23 months having the highest risk for anaemia and those aged 12-23 months at risk for ID and IDA. Conclusions: Anaemia, ID and VAD were high among rural women and their children in northern Benin, although ID accounted for a small proportion of anaemia. Multicentre studies in various parts of the country are needed to substantiate the present results, so that appropriate and beneficial strategies for micronutrient supplementation and interventions to improve food diversity and quality can be planned.