In studies worldwide, respiratory outcomes such as cough, wheeze and asthma have been consistently linked to mold exposure. Young children spend most of their time indoors and may be particularly vulnerable. We evaluated the associations between exposure to airborne fungal levels and episodes of wheezing in a cohort of 103 infants at risk for asthma (due to maternal history of asthma), living primarily in low-income urban settings. Using a new protocol that facilitates identification of rare and slow-growing fungi, we measured the type and concentration of cultured fungi in home air samples taken early in the infant's first year of life. We also inspected the homes for visible mold, water damage and other housing and environmental conditions. All homes had measurable indoor airborne fungi and 73%, had some sign of mold, water damage, dampness or a musty odor. One or more episodes of wheeze during the first year of life were observed in 38% of infants. Multiple logistic regression showed high indoor levels of Penicillium were a significant risk factor for wheeze (OR 6.18; 95% CI: 1.34-28.46) in the first year of life after controlling for season of sampling, smoking, endotoxin levels, day care attendance and confounders. Acrodontium, a rarely reported fungal genus, was detected in 18% of study homes, and was associated with wheeze in unadjusted models (OR 2.75; 95% CI 0.99-7.61), but not after adjustment for confounders. Total fungal levels, visually observed mold, dampness, water damage or musty odors were not significantly associated with wheeze.