A six-year-old girl from rural Bengal was admitted in our hospital with complaints of thirst, frequent micturition, pain in abdomen and constipation. Polyglandular endocrinopathies were identified in the girl thorough clinical and biochemical examination. Hashimoto’s thyroiditis along with Type 1 diabetes mellitus made her a candidate of Polyglandular Autoimmune disease type IIIA. Patient’s history revealed that she was on cow milk since birth. Presence of high risk alleles for T1DM HLA DQA1*0101-DQB1*0302 and DQA1*0301-DQB1*0501 in the girl was disclosed by genetic study. The effect of environmental factors along with genetic susceptibility might contribute to the aggravation and early expression of these rare autoimmune diseases in this girl. This could be a classic example of gene environment interaction in case of unexplained endocrinopathies.