Transient wheezing in young children has been reported to be independent of atopy. Although persistence of early wheezing has been associated with factors related to allergy in multiple studies, transient wheezing has not been similarly studied. The Childhood Allergy Study birth cohort was the source of these data. Transient wheezing was defined as history of wheezing in the past 12 months at ages 1, 2, and/or 4 years, but not at 6 years, and evaluated in relationship to aeroallergen-specific circulating IgE and positive skin testing as markers of an atopic profile. Testing for IgE and skin-prick testing to dust mites, dogs, cats, ragweed, and timothy were performed at the age of 6 years. Other variables in logistic regression analyses were sex; breast-feeding; birth order; parental allergy and smoking history; and household pets, daycare, fever, and antibiotic use in the 1st year of life. Of 372 children, 128 (34.4%) experienced transient wheezing and 175 (47.0%) never wheezed. Atopy was not associated with transient wheezing (adjusted odds ratio for a positive allergen-specific IgE test = 1.2, p = 0.66; skin-prick test = 0.8, p = 0.47). Boys were more likely to be transient wheezers (adjusted relative risk [RR] = 1.7; 95% confidence interval [CI], 1.1-2.8; p = 0.018). Transient wheeze was associated with antibiotic treatment in the first 6 months of life (adjusted RR = 1.6; 95% CI, 1.0-2.6; p = 0.048). We confirm previous observations that transient wheezing in young children is not associated with an atopic predisposition.