Specialized stromal tumors of the prostate encompass stromal sarcoma and stromal tumors of uncertain malignant potential (STUMP). The molecular signature associated with stromal sarcoma and STUMP has not been unraveled. The study was conducted to detect the chromosomal imbalances in stromal sarcoma and STUMP by using array comparative genomic hybridization (aCGH). The study consisted of two cases of stromal nodule, eight cases of STUMP (three degenerative atypia type, three myxoid type, one hypercellular type, and one phyllodes type), and four cases of stromal sarcoma, including a distant metastasis developed metachronously after a primary stromal sarcoma of the prostate. DNA was extracted from the representative paraffin-embedded formalin-fixed specimens and was submitted for aCGH. All stromal sarcomas and seven STUMPs revealed chromosomal aberrations. Overall, the most common alteration was loss of chromosome 13 (10 cases), followed by loss of chromosome 14 (9 cases), and loss of chromosome 10 (7 cases). Except one stromal sarcoma, which showed a distinct chromosomal profile of multiple amplifications, other stromal sarcomas showed a similar pattern to those of STUMP. Stromal sarcoma and STUMP shared similar profiles of chromosomal imbalances. From a molecular genetic perspective, the recurrent chromosomal alterations support the concept of specialized stromal tumors of the prostate as a distinctive tumor entity.