OBJECTIVE To compare the efficacy of two tests, alkaline phosphatase (AP) and skeletal alkaline phosphatase (SAP) as staging markers to discriminate patients with cancer of the prostate (CaP) with bone metastases (M+) from those without bone metastases (Mo). METHODS Patients with previously untreated CaP were entered in the retrospective analysis. Serum concentrations of AP (n = 215) and SAP (n = 73) were available. After staging the patients could be divided into 2 groups: Group I: patients with CaP and bone metastases (cT2-4 NxMoss AP: n = 40; SAP: n = 21) Group II: patients with CaP without bone metastases (cT3-4 Nx Mo; pT1-3 No Mo; AP: n = 175; SAP: n = 52). RESULTS None of the Mo patients but 71% of the M+ patients exhibited a SAP value above the reference range (< 19 ng/ml). This difference is statistically significant (p < 0.001) and resulted in a sensitivity and specificity of 71% and 100%, respectively. The Youden-index is 0.7. In contrast 7% of the Mo patients and only 13% of the M+ patients exhibited a AP value above the reference range (< 170 U/l). This difference is statistically not significant (p = 0.71) and resulted in a sensitivity and specificity of 13% and 93%, respectively. The Youden-index is 0.06. CONCLUSIONS SAP could become a useful marker in the evaluation of patients with newly diagnosed CaP as it provides more information than AP concerning the skeletal status of these patients.