Prostate cancer is the most common cancer among men. The prospective discrimination of aggressive and clinically insignificant tumors still poses a significant and, as yet, unsolved problem. PITX2 DNA methylation is a strong prognostic biomarker in prostate cancer. Recently, a diagnostic microarray for prostate cancer prognosis based on PITX2 methylation has been developed and validated. Because this microarray requires nonstandard laboratory equipment, its use in a diagnostic setting is limited. This study aimed to develop and validate an alternative quantitative real-time PCR assay for measuring PITX2 methylation that can easily be established in clinical laboratories, thereby facilitating the implementation of this biomarker in clinical practice. A methylation cut-off for patient stratification was established in a training cohort (n Z 157) and validated in an independent test set (n Z 523) of men treated with radical prostatectomy. In univariate Cox proportional hazards analysis, PITX2 hypermethylation was a significant predictor for biochemical recurrence (P < 0.001, hazard ratio Z 2.614). Moreover, PITX2 hypermethylation added significant prognostic information (P Z 0.003, hazard ratio Z 1.814) to the Gleason score, pathological T stage, prostate-specific antigen, and surgical margins in a multivariate analysis. The clinical performance was particularly high in patients at intermediate risk (Gleason score of 7) and in samples containing high tumor cell content. This assay might aid in risk stratification and support the decision-making process when determining whether a patient might benefit from adjuvant treatment after radical prostatectomy. (J Mol Diagn 2013, 15: 270e279; http://dx.doi.org/10.1016/j.jmoldx.2012 In the western world, prostate cancer is by far the most common cancer and also one of the leading causes of cancer-related deaths among men.1 However, because of the relatively good prognosis of prostate cancer, only a relatively low percentage of men diagnosed as having localized prostate cancer will die of it. Prostate-specific antigen (PSA) screening for prostate cancer allows for early detection of prostate cancer and, regardless of the limitations of PSA and the problem of overdiagnosis, saves lives.