Variations in the sero-prevalence of antibody to brucella infection by cow, farm and area factors were investigated for three contrasting districts in Kenya: Samburu, an arid and pastoral area: Kiambu, a tropical highland area; and Kilifi, a typical tropical coastal area. Cattle were selected by a two-stage cluster sampling procedure and visited once between August 1991 and 1992. Schall's algorithm, a statistical model suitable for multi-level analysis was used. Using this model, older age, free grazing and large herd size (> or = 31) were associated with higher seroprevalence. Also, significant farm-to-farm, area-to-area and district-to-district variations were estimated. The patterns of high risk districts and areas seen were consistent with known animal husbandry and movement risk factors, but the larger than expected farm-to-farm variation within high risk areas and districts could not be explained. Thus, a multi-level method provided additional information beyond conventional analyses of sero-prevalence data.