Prostatic basal cell is thought to play a pivotal role in hyperplastic change or carcinogenesis of prostate by their proliferation and stem cell transformation. We investigated stem cell transformation of basal cell hyperplasia observed at biopsy specimens after High Intensity Focused Ultrasound (HIFU) therapy for early stage prostate cancer. Patients and Methods: Basal cell hyperplasia was observed at biopsy specimens in two patients after HIFU therapy. Of these patients, one showed cancer recurrence. Specimens were studied with usual HE, and immunohistochemical studies for prostate specific antigen (PSA), stem cell markers such as CD44, CD117 (c-kit), CD133 and Vimentin. Results: Both basal cell hyperplasia cases indicated PSA (−), CD44 (++), CD117 (−), Vimentin (−) and one specimen showed CD133 (++). Basal cell hyperplasia was presumed to appear during the regeneration process of normal prostate tissue after HIFU therapy, when basal cell proliferated and transformed to acinal cells through epithelial to mesenchymal transition.