BACKGROUND: Three-quarters of the burden of mental health problems occurs in low-and-middle-income countries, but few epidemiological studies of these problems in preschool children from sub-Saharan Africa have been published. Behavioural and emotional problems often start in early childhood, and this might be particularly important in Africa, where the incidence of perinatal and early risk factors is high. We therefore aimed to estimate the prevalence and risk factors of behavioural and emotional problems in young children in a rural area on the Kenyan coast. METHODS: We did a population-based epidemiological study to assess the burden of behavioural and emotional problems in preschool children and comorbidities in the Kilifi Health and Demographic Surveillance System (KHDSS, a database formed of the population under routine surveillance linked to admissions to Kilifi County Hospital). We used the Child Behaviour Checklist (CBCL) to assess behavioural and emotional problems. We then determined risk factors and medical comorbidities associated with behavioural and emotional problems. The strength of associations between the risk factors and the behavioural and emotional problems was estimated using generalised linear models, with appropriate distribution and link functions. FINDINGS: 3539 families were randomly selected from the KHDSS. Of these, 3273 children were assessed with CBCL. The prevalence of total behavioural and emotional problems was 13% (95% CI 12-14), for externalising problems was 10% (9-11), and for internalising problems was 22% (21-24). The most common CBCL syndrome was somatic problems (21%, 20-23), whereas the most common DSM-IV-oriented scale was anxiety problems (13%, 12-14). Factors associated with total problems included consumption of cassava (risk ratio 5.68, 95% CI 3.22-10.03), perinatal complications (4.34, 3.21-5.81), seizure disorders (2.90, 2.24-3.77), and house status (0.11, 0.08-0.14). Seizure disorders, burn marks, and respiratory problems were important comorbidities of behavioural and emotional problems. INTERPRETATION: Behavioural and emotional problems are common in preschool children in this Kenyan rural area and are associated with preventable risk factors. Behavioural and emotional problems and associated comorbidities should be identified and addressed in young children. FUNDING: Wellcome Trust.