The class-3 semaphorins (Sema3A-F, Sema3s) are initially identified to play an important role in axonal guidance and cell migration. Our previous studies showed that Sema3s are also involved in the lymph node metastasis of prostate cancer, and are likely to modulate the behavior of prostate cancer with a pro-tumoral or an anti-tumoral effect, depending on their subtypes. However, no study has critically investigated the value of Sema3s expression in preoperative biopsy samples for the prediction of biochemical recurrence (BCR) after radical prostatectomy. In this study, we evaluated Sema3s expression by immunohistochemistry on 198 prostate biopsies with low- and intermediate-risk localized prostate cancer. The median follow-up was 42 months (range, 6-60) for all patients. Our results showed that Sema3A (OR: 0.19, P<0.001), Sema3B (OR: 0.38, P=0.003), Sema3E (OR: 0.39, P=0.007), and Sema3C (OR: 2.31, P=0.014) staining were independent predictors of BCR on multivariable analysis. Sema3A, 3B, 3C and 3E expression demonstrated potential values in predicting BCR upon survival analysis (P=0.001, P=0.003, P=0.029, P=0.037, respectively, Log-rank test). Our findings suggested that Sema3A, 3B, 3C, and 3E immunostaining in prostate biopsies, as supplements to clinicopathological parameters, could be used for predicting BCR in low- and intermediate-risk prostate cancer patients after radical prostatectomy. Specially, concurrent Sema3C-positive and Sema3A-negative, 3B-negative, 3E-negative staining is associated with an adverse prognosis. Further prospective studies in larger patient populations are needed to validate the current observations.