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. The gene discussed is KLK3; the disease is prostate cancer.