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Background: Patients who suffer from traumatic peripheral nerve injuries receive temporary treatment after referring to hospital. Peripheral nerve repair surgery in some patients is done immediatly after damage but many of them get secondary nerve repair after longer periods of time. In this study we have compared the clinical and electrodiagnostic outcome among primary and secondary nerve repair. Methods: Patients with primary or secondary repair of median and ulnar nerves were enrolled in a non-randomized clinical trial prospective study. Information used in this study was collected from patients that passed a surgery to repair the peripheral nerve betwen years 2003 to 2010 in Alzahra and Ayatollah Kashani hospitals of Isfahan, Iran. Patients were followed by clinical and electrodiagnostic examination in the third, sixth, twelfth and eighteenth month after surgery and the outcome of recovery in their hand function (sensory and motor) were evaluated. Findings: 122 patients (64 men and 58 female) were enrolled in this study. 56 patients (45.9%) had a primary repair surgery and 66 patients (54.1%) had a secondary repair surgery. The age range were between 7 to 55 years (mean: 24.9 ± 8.9), with the mean of 25.6 ± 7.1 for primary group and 24.4 ± 9.8 for secondary group (P = 0.59). By using the Maan-Whitney test, primary group had better clinical sensory and motor recovery and also improvement in sensory NCV (Nerve conduction velocity) and EMG (Electromyogram) findings compared with secondary group (P < 0.05), but no significant difference was seen in motor NCV between 2 groups (P = 0.1). Conclusion: In this research we studied the result of primary and secondary repair in both median and ulnar nerve injuries. We concluded that clinical and electrodiagnostic outcome in primary nerve repair were better than secondary nerve repair, thus we suggest immediate repair after peripheral nerve injuries, when possible. [ABSTRACT FROM AUTHOR]