Mouse allergen has emerged as an under recognized indoor allergen associated with sensitization and contributing to asthma severity. As part of a study of farm residence, exposures, and risk of allergic diseases in children in New Zealand, 216 living room floor dust samples were analysed for the mouse allergen, Mus m 1. Associations between Mus m 1 and allergic diseases, farm residence, and presence of cats were analysed. Significantly higher levels of Mus m 1 were found in farm dwellings, while the presence of cats was associated with significantly lower Mus m 1 levels. Levels of Mus m 1 in New Zealand were considerably lower than those reported overseas. No significant associations were found between Mus m 1 levels and atopic status or allergic diseases. Mouse allergen is unlikely to be an important indoor allergen for rural New Zealand children.