Abstract Background Allergic status has been strongly influenced by early exposures; however, allergic diseases are hard to measure in early life. Thus, this study proposed a latent variable allergy traits around the second year of life and analyzed pre- and perinatal factors associated with this phenomenon. Methods The study used data from the BRISA birth cohort, Ribeirão Preto, Brazil (n = 3644). The theoretical model included: family allergy (history of allergic rhinitis, atopic dermatitis, and asthma); gestational period variables (socioeconomic status, mother’s skin color, pregestational body mass index – BMI, smoking, gestational diabetes, and hypertension); birth variables (gestational age, 5-minute Apgar score, birth weight, type of delivery), and early life factor (exclusive breast feeding). The outcome was allergy traits around the 2nd year of life, a latent variable deduced from the shared variance among medical diagnosis of allergic rhinitis, atopic dermatitis, and food allergy. The model was analyzed by structural equation modeling. Results Higher socioeconomic status (SC = 0.256; p