In Benin herders are confronted with a number of infectious diseases whose epidemiology remains unclear. The objective of the present study was to assess cattle keepers’ perception on municipalities of Benin at higher risks of the most important infectious diseases that affect dairy cattle. A total of 114 cattle keepers were enrolled from 12 municipalities known for their high dairy production in the country and their neighbouring municipals. Data were collected from August 2013 to January 2014 and subjected to a principal component analysis (PCA) followed by an ascending hierarchical classification (AHC). The study revealed that the most important infectious diseases that affect milk production according to herders are dermatophilosis, Foot-and-Mouth disease and CBPP. Tchaourou (in the North) and Dassa-Zoume (in the Centre) were reported as municipalities at higher risks of contamination. The estimation of the prevalence of these diseases and the identification of their associated risk factors is needed for devising adequate control strategies.