Background: Hypospadias is a fairly common problem, and it is the most common genital congenital anomaly. Objective: This study was carried out to compare polyglactin and polydioxanone in hypospadias repair by assessing the rate of complications, especially urethrocutaneous fistula (UCF) formation. Patients and Methods: This is a prospective observational cross-sectional hospital-based study carried out at the Department of Paediatric Surgery, Ribat University Hospital, from June 2015 to November 2016. In Group A, there were 55 patients who underwent repair using polyglactin, and in Group B, there were 50 patients who underwent repair using polydioxanone. All patients were operated by the same surgeon. Results: The mean age of Group A was 5.7 ± 4.3 years and 5.1 ± 3.9 years in Group B. Meatal advancement and glanuloplasty incorporated operation was done in 47.6%, Tubularized incised plate urethroplasty in (31.4%), Theirsch-Duplay in 20% and Mathieu's repair in 1%. The complication rate was 34% in Group A and 10.9% in Group B. The most frequent complication was UCF, as 19 patients (18.1%) of the study candidates developed UCF; most of them were in Group A (14 patients) and 5 patients in Group B. Another significant complication was meatal stenosis, which occurred in 11 patients (10.5%): 9 in Group A and 2 in Group B. Conclusion: Polydioxanone (PDS) is satisfactory in hypospadias repair as it is associated with better outcome, especially UCF, which is most common and most difficult to treat complication.