The identification of new diagnostic markers and potential treatment targets for prostate carcinoma (PCa) necessitates the evaluation of expression patterns in both malignant and non-malignant tissue specimens. In this study, we compared the mRNA expression of recently identified prostate-associated genes, prostate stem cell antigen (PSCA) and transient receptor potential p8 (trp-p8), to the mRNA expression of the most commonly used markers for PCa, prostate-specific antigen (PSA) and human kallikrein 2 (hK2). For these four candidates we performed highly specific quantitative real-time LightCycler RT-PCR assays with cDNA originating from matched tissue specimens of 40 patients with primary PCa. The highest transcript amounts were found for PSA in malignant as well as in non-malignant tissue specimens followed by hK2, trp-p8 and PSCA with an mRNA expression remarkably lower. The relative transcript levels of PSA, hK2 and trp-p8 were elevated in malignant in comparison to non-malignant tissues, but only for trp-p8 this increased expression was statistically significant. Focussing on organ confined tumors, we found a significant difference of the mRNA expression of PSA and trp-p8 between malignant and non-malignant tissue specimens. The marker trp-p8 is also suited to differentiate between the tumor stages when quantifying its transcript levels within tumor tissue specimens. The evaluation of the mRNA expression patterns of these markers by quantitative real-time RT-PCR could provide new tools for differential diagnosis and molecular staging. According to our data, the novel marker trp-p8 seems to represent a highly prostate-specific and PCa-associated gene qualifying it as a potential target for specific therapies.