An eleven-year-old Japanese boy was admitted to our hospital for evaluation of decreased growth velocity (0.7 cm/year) of two years. He also suffered from poor appetite, cold intolerance and slow body movements. Physical examination revealed myxedematous face and dry and cold skin but no goiter. His height was 138.8 cm (-1.0 SD), body weight 38.0 kg (+16.5%), and body temperature 35.4°C. His serum free-thyroxine (f-T4) was 0.06 ng/dl, free-triiodothyronine (f-T3) was 100 pg/dl, while TSH was 254.4 μU/ml. He was positive for anti-microsome antibody (AMA), anti-thyroglobulin antibody (ATA), thyrotropin-binding inhibitor immunoglobulins (TBII) and thyroid stimulation blocking antibody (TSBAb). Thyroid 24-hour radioiodine uptake was less than 1%. This patient was therefore diagnosed as having atrophic autoimmune thyroiditis (AAT), and replacement therapy with l-thyroxine was initiated. We also analyzed the HLA haplotypes and thyroid function of his family. The patient's HLA haplotypes were A2, A4, B62, B46, Cw1, Cw4, DR4 and DR8. All of his family members had normal thyroid function, but his mother was positive for anti-microsome antibody. We describe a rare case of AAT with positive TBII and TSBAb in a prepubertal boy. Accumulation and comparison of similar cases may facilitate our understanding of the autoimmune mechanisms in the pathogenesis of childhood AAT.