The histologic criteria and selective biomarkers of prostate ductal type adenocarcinoma (DAC) are relatively unknown compared to that known about acinar type adenocarcinoma (AAC). It is known that genetic alteration in Hox13 gene is associated with carcinogenesis of prostate cancer. In this study, we investigated clinicopathologic characteristics of HoxB13 expression in prostate cancer and compared clinicopathologic profiles of DAC and AAC of prostate. After slide review, some morphological variants of DAC, equivalent to Gleason pattern 3 and 5 of AAC were identified. High level of HoxB13 expression was identified in 46.5% (46 out of 99 cases) and 39.2% (31 out of 79 cases) of cases that belong to the training set and test set, respectively. In the training set, high level of HoxB13 expression was significantly correlated with DAC (P < 0.001), higher Gleason score (P < 0.001), advanced pathologic T stage (P = 0.010), and occurrence of biochemical recurrence (BCR; P < 0.001). The test set confirmed that high level of HoxB13 expression was associated with DAC (P < 0.001), higher Gleason score (P = 0.001), advanced pathologic T stage (P < 0.001), and occurrence of BCR (P < 0.001). Our findings suggest that HoxB13 may be a useful diagnostic marker for detection of DAC and a prognostic marker for prediction of BCR.