Mice in buildings are a hygiene hazard because they harbour several zoonoses and animals diseases. The aim of this study was to gather information on specific bacteria in house mice caught in the urban environment. Mice caught in snap traps during pest control activities were collected in and around the city of Utrecht, the Netherlands, during May - June 2014, October - November 2015 and September - November 2016. The gut contents were analysed for ESBL/AmpC-producing Enterobacteriaceae, Salmonella spp., and Clostridium difficile and the buccal cavities were swabbed for MRSA. In total 109 house mice (Mus musculus) and 22 wood mice (Apodemus sylvaticus) were examined. One mouse was positive for Enterobacter spp. Salmonella spp. and MRSA were not found. Of n = 80 mice, 35.0% carried C. difficile (ribotypes in descending order of frequency: 014/020, 258, 002, 005, 013, 056, 081, and two unknown ribotypes). In conclusion, mouse droppings are a hazard for transmission of C. difficile to humans and their environment. This article is protected by copyright. All rights reserved.