We found that positive lymph node metastasis (HR:10.54, 95% CI:2.94–37.80, P < 0.001) and preoperative PSA (HR:1.27, 95% CI:1.11–1.46, P = 0.001) were independent factors of poor prognosis in prostate cancer, while high TLR9 expression were not an independent factor for predicting prognosis. This evidence concerns the gene TLR9 and Familial prostate cancer.