This study was designed to compare and evaluate the presence of engrailed-2 (EN2) protein in urine collected before and after prostate massage as a diagnostic marker for prostate cancer (PCa). We analysed and compared 76 urine samples (38 before and 38 after prostate massage) from the benign group (BPH) and 66 urine samples (33 before and 33 after prostate massage) from patients with PCa confirmed by prostate biopsy. EN2 levels from the PCa and men with BPH (age range 50–82) were related to the tumour stage, Gleason score and prostate-specific antigen. EN2 levels were determined by enzyme-linked immunosorbent assay in urine. The median EN2 levels in urine after prostate massage were significantly different from those determined in urine before prostate massage (1.25 ng/ml in the PCa group and 0.34 ng/ml in the BPH). The mean EN2 levels in PCa patients were 3.76-fold higher than those in non-PCa patients after prostate massage. The distinct influence of prostate massage on EN2 levels was found to be related to the Gleason score and tumour stage. EN2 may be considered a marker of PCa with certain limitations, such as those related to tumour staging. The specificity and sensitivity of the protocol are highly dependent on prostate massage.