The data shown in Section 1.1 of this article provide detailed information on the veterinary clinics that participated in a recent survey of the prevalence of fecal shedding of Clostridium perfringens and C. difficile by dogs and cats which was carried out in the Madrid region (Spain) . Furthermore, the demographic and clinical features of recruited animals are detailed in Section 1.2, and Section 1.3 provides extensive data on the genetic and phenotypic characteristics of recovered bacterial isolates.