Antibodies against high molecular weight cytokeratin (34betaE12) and p63 are frequently used basal cell markers to aid in the diagnosis of prostate cancer (Pca). Absence of a basal cell marker in an atypical lesion histologically suspicious for cancer supports a diagnosis of Pca. However, absence of basal cells demonstrable by basal cell immunohistochemistry (IHC) is not always conclusive for PCa. Some benign prostatic lesions may have inconspicuous or even lack basal cell lining focally. Technical factors such as tissue fixation and antigen retrieval techniques may also make the detection of basal cells difficult. Improving the sensitivity of current basal cell markers is critical if these tests are being used to help make diagnostic decisions in conjunction with standard histology. In this study, we test the hypothesis that that inclusion of both 34betaE12 and p63 in the same IHC reaction (basal cell cocktail) is advantageous over either marker used alone. One thousand three hundred fifty glands from 9 trans-urethral resectioned of prostate specimens with benign prostatic hypertrophy were used to study the immunostaining intensity and pattern for 34betaE12, p63, and the basal cell cocktail. Basal cell marker expression was scored as strong, moderate, weak, or negative. Basal cell staining was considered complete if 75% of the gland's circumference was positive for the basal cell marker and partial if <25% of the circumference was stained. The mean staining intensity and variance were calculated for 34betaE12, p63, and the basal cell cocktail. A paired test was used to evaluate whether the overall basal cell staining was significantly different between 34betaE12, p63, and the basal cell cocktail. F-test was used to assess the variances for 34betaE12, p63, and the basal cell cocktail. A high-density tissue microarray (TMA) comprising prostate tissue from 103 tumors from men with clinically localized Pca and a separate TMA comprising metastatic hormone-refractory Pca samples from 23 rapid autopsy cases were used to study the aberrant expression of 34betaE12 and p63 in clinically localized and poorly differentiated Pca. The prostate glands in transition zone have variable basal cell staining intensity and pattern with 34betaE12, p63, or the cocktail. Histologically, benign glands lack basal cell lining in 2%, 6%, and 2% of glands with cocktail, 34betaE12, and p63 staining, respectively. The staining variance for the cocktail is significantly smaller than that for 34betaE12 (0.0100 vs 0.1559, p = 0.0008). It is also smaller than that for p63, although a statistical significance has not been reached (0.0100 vs 0.0345, p = 0.099). The basal cell cocktail stains the basal cell layers more intensely than either 34betaE12 or p63 alone, with complete and partial strong basal cell staining in 93% and 1% of benign glands, compared with 55% and 4% with 34betaE12 and 81% and 1% with p63. Complete and partial weak staining is seen in 0% and 0% of benign glands with basal cell cocktail, compared with 8% and 7% with 34betaE12 and 4% and 1% with p63 (p = 0.007 and 0.014 for cocktail vs 34betaE12 and cocktail vs p63, respectively). A total of 2.8% clinically localized Pca had positive 34betaE12 staining and 0.3% had positive p63 staining. Five (22%) of the metastatic Pca is positive for 34betaE12. However, none had p63 expression. The basal cell cocktail had a staining pattern identical to that of 34betaE12. IHC of the prostatic glands from the transition zone is subjected to staining variability that results in frequent variable and occasional negative basal cell staining in histologically benign glands; 34betaE12 is most susceptible, and basal cell cocktail is least susceptible to such variability. Basal cell cocktail not only increases the sensitivity of the basal cell detection, but also reduces the staining variability and therefore renders the basal cell immunostaining more consistent. We recommend this basal cell cocktail for routine Pca diagnostic work-up.