Multiple factorial analysis (MFA) and hierarchical cluster analysis (HCA) were used to differentiate husbandry practices relevant to contagious disease risk in Malagasy smallholder pig farms. Data from 709 pig farms collected in three study areas were included in the analysis, with variables describing husbandry practices organized in six groups: structure of the farm, animal-contacts, person- and vehicle-contacts, feeding, sanitary aspects, and supplementary variables. The results of the MFA showed that the husbandry practices differed greatly between regions. The HCA identified groups of farms within two regions and suggested variation in professional standards amongst the pig farmers. These differences can be partially explained by variation in: access to professional expertise and technical support, training in farm management and control of diseases, and presence of farmers' associations. Control measures and communication need to be adapted accordingly to reduce the risk of pig diseases in smallholder Malagasy production.