Background: Cow milk allergy (CMA) is the most common food allergy in breastfed infants. The aim of this study is to verify whether certain perinatal factors may influence the development of CMA immunoglobulin E (IgE)+. Methods: A retrospective, observational study of case and control groups was carried out. Information was collected of patients with CMA IgE+ from our department during the years 1990-2013. Patients of the same age and sex were recruited for the control group. Information on the following variables was collected: sex, age, pregnancy tolerance, duration of pregnancy, type of delivery, isolated doses of formula feeding in hospital (FFH), duration of breastfeeding, and family history of allergy (defined as ≥1 first-degree family member with allergic disease). Statistical analysis was performed using multivariate logistic regression techniques. Results: A total of 211 cases were included in this study. Multivariate analysis showed an influence of duration of breastfeeding, FFH to be a risk factor (OR 4.94; 95% CI 2.68-9.08), especially in caesarean delivery (OR 11.82; 95% CI 2.64-47.50), and prematurity (OR 0.29; 95% CI 0.09-0.92) to be a protective factor. Conclusions: Perinatal factors play a key role in the development of CMA IgE+, with an influence of breastfeeding duration, FFH and caesarean delivery as risk factors and prematurity as a protective factor. While family history had no important role, environmental factors were more decisive.