Background Pre or postnatal exposure to pesticides can result in immune system disorders and development of allergic diseases. The study evaluates the association between breast milk organochlorine pesticide (OCP) levels and development of allergic diseases in the first year of life. Methods The study involved 93 infants and their mothers. Breast milk samples were collected within the first six months of birth and were analysed for the presence of six OCP residues (Endrin, DDD, DDT, DDE, Heptachlor, Lindane) using high-performance liquid chromatography and an acetylcholinesterase-based chronoamperometric biosensor. Infants were monitored for 12 months for any signs of allergies. Results 28 samples contained at least one of the six OCP residues, with Endrin being the most frequently detected OCP at 25.8%. Heptachlor had the highest mean estimated daily intake (EDI) value of 2.42 x10 -3 and the highest mean hazard quotient (HQ) of 4.84. EDI of Endrin, DDE, DDD, and Heptachlor exceeded provisional tolerable daily intake (PTDI) levels in 9, 7, 11, and 11 infants, respectively. The presence of OCP residues in breast milk was not significantly associated with any type of allergy, including food allergies, rhinitis, wheezing episodes, or eczema in the first year of life. Conclusion Even though calculated HQ and EDI values higher than PTDI values are a matter of concern for health, no significant association between breast milk OCP’s and allergic diseases in the first year of life are shown in the present study.