The nature of tubulocystic carcinoma, a rare renal tumor composed of tubular and cystic structures, is poorly understood. It has been suggested that it may represent a low-grade collecting duct carcinoma of the kidney despite the lack of sufficient molecular and pathologic evidence. The aim of this study was to examine the clinical and pathologic features of 13 cases of tubulocystic carcinoma of the kidney. Furthermore, using gene expression microarray analysis, we defined the molecular signature of this tumor by comparing it with other renal tumors in our previously established molecular profile database. Histologically, all 13 tumors were composed of closely packed tubules and cysts of varying sizes separated by fibrovascular septa. The epithelial lining cells of the tubules and cysts in this tumor were characterized by abundant eosinophilic cytoplasm with prominent nucleoli often showing a hobnail appearance. Clinically, one of the 13 cases showed metastasis to the pelvic lymph nodes. Five of the 13 cases coexisted with papillary renal cell carcinoma (RCC) (n=3) or papillary adenoma (n=2). In addition, the molecular profile of tubulocystic carcinoma was similar but not identical to those of papillary RCC by clustering analysis. Through comparative genomic microarray analysis, tubulocystic carcinoma showed gains of chromosome 17, but not chromosome 7, whereas most papillary RCCs showed chromosomal gains in both 7 and 17 (trisomies). Therefore, based on its unique pathologic features and molecular signature as well as its biologic behavior to develop metastasis either by itself or in association with papillary RCC, tubulocystic carcinoma of the kidney should be recognized as a distinct subtype of RCC and be distinguished from other malignant and benign cystic lesions of the kidney.