Primary peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) of the thyroid is an extremely rare neoplasm. Six cases of primary PTCL-NOS of the thyroid were analysed for clinicopathological features and genomic alteration patterns using oligo-array comparative genomic hybridization. All patients had a diffusely enlarged thyroid and three cases showed leukaemic manifestation. Five of the six cases had anti-thyroid antibodies and the remaining case showed hypothyroidism, suggesting that all cases had autoimmune thyroiditis. Except for one early relapsed case, the remaining five patients are alive and three of these five individuals have survived for 70 months or more. Interestingly, two cases showed spontaneous regressions after partial thyroid biopsy without any therapy. Leukaemic manifestation disappeared after irradiation of the thyroid mass in another two cases. The tumour cells were positive for CD3, CD4 and CXCR3 in all cases, suggesting that the tumour cells are of a type 1 helper T-cell origin. All six cases showed genomic alterations that were different from those previously reported for PTCL-NOS. The loss of 6q24·2 was characteristic and was detected in four of the six cases. These results suggest that primary PTCL-NOS of the thyroid arising from autoimmune thyroiditis is a distinct disease entity among heterogeneous PTCL-NOS.