Objective To explore the clinical value of the serum prostate specific antigen (PSA), serum alkaline phosphatase (ALP), serum bone specific alkaline phosphatase (BAP) and Gleason score in patients with newly diagnosed prostate cancer to predict positive bone metastasis results of radionuclide bone scintigraphy. Methods The serum levels of PSA, ALP, BAP and Gleason scores in 212 patients with newly diagnosed prostate cancer were detected. The relationship between results of radionuclide bone scintigraphy and its PSA, ALP, BAP and Gleason scores were analyzed. Results The single variance analysis showed that serum PSA, ALP, BAP and Gleason score could independently predict positive bone metastasis in radionuclide bone scintigraphy. Multivariance analysis suggested that serum PSA>50ng/mL, serum ALP>1000μg/L, serum BAP>20.1μg/L and Gleason score 7-10 points were risk factors for positive bone metastases outcome in bone scintigraphy, which had predictive value. The low probability was found in patients with PSA<15ng/mL, serum ALP<130μg/L, serum BAP<20μg/L and Gleason score <7, which can be combined with the clinical situation in the consideration of a bone scintigraphy. Conclusion In addition to PSA and Gleason score, serum ALP especially BAP could also be considered as a prediction index to measure the risk of newly diagnosed prostate cancer patients with bone metastasis.