We performed repetitive molecular staging using, nested rt-PCR for PSA and PSM at the peripheral blood (PB) and bone marrow (BM) of patients with prostate cancer (Pr.Ca) and benign prostate hyperplasia (BPH) after transrectal ultrasonography-guided biopsy (TRUS-B; 6-9 biopsies/patient), Pr.Ca patients after radical prostatectomy (RP), and Pr.Ca patients with diffuse bony metastases. All BPH patients (N = 20) tested negative at BM. Of the 2 who tested positive at PB 2 weeks after TRUS-B tested negative 8 weeks after TRUS-B. Of the 17 Pr.Ca, 7 (41.2%) tested positive at PB for PSA and PSM 2 weeks after TRUS-B while only 4 (23.5%) of them tested positive at repetitive analysis 8 weeks after TRUS-B. Two (11.8%) of the 17 Pr.Ca patients had positive analysis at BM for PSA and PSM 2 and 8 weeks after TRUS-B. Of 12 Pr.Ca patients with negative pre-operative molecular staging, 7 (58.3%) tested positive at PB for PSA and PSM 2 months post-RP but only 3 (25%) of them re-tested positive 12 months post-RP. Of these 12 Pr.Ca, 4 (33.3%) tested positive at BM for PSA and PSM 2 months post-RP while none re-tested positive 12 months post-RP. All Pr.Ca (N = 20) with diffuse bony lesions tested positive at BM. At PB, 6 of them (30%) tested negative for both PSA and PSM. Our data suggest that nested rt-PCR for PSA and PSM at PB is affected by TRUS-B and RP, while such analysis at BM concerted diffuse bony disease.