Background: Mouse allergen exposure is prevalent among urban children with asthma. Little is known about mouse allergen exposure in children at risk for the development of allergic diseases. Aims of the study: To assess indoor mouse allergen exposure in early life among children with parental history of asthma or allergies. Methods: Prospective birth cohort study of 498 children with a history of allergy or asthma in at least one parent living in metropolitan Boston. Results: Of the 498 participating children, 357 (71.7%) resided outside the city of Boston and 439 (90.7%) lived in households with incomes >$30 000. Mouse allergen was detected in 42% of the homes of study participants. In a multivariate analysis adjusting for sex, income, and endotoxin, black race [odds ratio (OR) = 3.0; 95% confidence interval (CI) = 1.3–6.6, P = 0.009], signs of mice in the home at age 2–3 months (OR = 3.0; 95% CI = 1.6–5.6, P = 0.0006), and kitchen cockroach allergen levels ≥0.05 to <2 U/g (OR = 1.8; 95% CI = 1.1–3.2, P = 0.02) were associated with detectable mouse allergen in the kitchen. In this model, living in a single detached house was inversely associated with detectable kitchen mouse allergen levels (OR = 0.4; 95% CI = 0.2–0.6, P = 0.0001). Conclusion: Infants with a parental history of asthma or allergies are commonly exposed to mouse allergen in their homes. Among infants at high risk for atopy, predictors of increased mouse allergen levels included black race, reported mice exposure, and moderate levels of cockroach allergen.