Previous studies of mouse allergens and laboratory-animal-worker-related allergy and asthma suggest that quantifying mouse allergen levels in homes could augment our understanding of inner-city asthma. We hypothesized that levels of mouse allergen in inner-city homes would be related to certain household characteristics. Dust samples were collected from the kitchens and beds of 221 mothers enrolled in a prospective birth cohort study, 92 of African American and 129 of Dominican ethnicity. Samples were analyzed for mouse urinary protein. The geometric mean for kitchen samples was 4.6 micro g/g [95% confidence interval (95% CI), 3.2-6.5] and for bed samples was 0.9 micro g/g (95% CI, 0.8-1.1). The variables associated with mouse allergen levels in the home were frequency of mouse sightings, use of traps or pesticides for mice, presence of holes in ceilings or walls, absence of a cat, and living in a building with fewer than eight floors. Statistically significant neighborhood differences in levels of mouse allergen and report of rodents in the home were also observed. In conclusion, mouse allergen was prevalent among inner-city apartments, and the positive predictive value of self-reported frequent mouse sightings was high (90% for kitchens). However, high levels of mouse allergen were also found in many homes where mothers reported never seeing mice.