The present study was designed to analyze the distribution of HLA DQ B1* and DR B1* in patients with goitrous juvenile autoimmune hypothyroidism from Hyderabad, India. Analysis indicated an increase in the frequencies of HLA DQ B1* 03 allele (P < 0.000) and HLA DR B1* 04 (P < 0.05) alleles in this group of patients when compared to the controls, whereas the frequency of DQB1* 05 was found to be decreased in patients' group compared to the controls (p < 0.01). To conclude, we report a positive correlation between DQ B1* 03 and DR B1* 04 and goitrous juvenile autoimmune hypothyroidism, whereas DQB1* 05 is observed to be negatively correlated with this thyroid dysfunction. Since the disease-susceptible HLA class II alleles appear to differ in various ethnic groups for some autoimmune diseases, the observed association from Indian series of patients holds significance.