In a prospective study, the outcomes of microsurgical varicocelectomy in men with primary versus secondary infertility were compared. Ninety-two infertile men with a varicocele were included. They were classified into those with primary infertility (n = 57) and secondary infertility (n = 35). Clinical data, semen parameters and scrotal ultrasound finding were available for all patients and microsurgical varicocelectomy was performed on all of them. Spontaneous pregnancy rates and improvement in semen parameters in those men with primary versus secondary infertility were recorded 1 year after surgery. Preoperatively, there was no significant difference in the mean semen parameters in both groups (p > 0.05) and the mean semen parameters showed no significant difference between men with primary and secondary infertility. After microsurgical varicocelectomy, the mean semen parameters improved significantly in both group (p < 0.05 for each), but there were no significant difference in mean semen parameters between men with primary versus secondary infertility (p > 0.05 for each). After adjustment for patient and partner ages, the pregnancy rate at the end of the follow-up period did not significantly differ between the primary (24/57, 42.1%) and secondary (11/35, 31.4%) infertility group (Pearson's Chi-squared = 1.05). We concluded from this study that semen parameters and pregnancy rates after microsurgical varicocelectomy were similar between men with primary and secondary infertility.