Introduction: Repair of the penile urethra in hypospadias is done with different suture materials. The aim of this study was to quantify the impact of different suture threads on histological parameters of the penis and urethra following hypospadias repair in rats. Materials and Methods: Six groups of the rats, except for the control group, underwent incision and repair of the penis and urethra in the ventral line using different suture materials including Chromic, Vicryl (polyglactic acid), PDS (polydioxanone), Rapid Vicryl (polyglactin 910), Monocryl (poliglecaprone 25) and control groups. After 3 weeks the body of the penis was excised and histological sections were studied using stereological methods. Results: Monocryl (poliglecaprone 25) was associated with a higher percentage of vessel density, higher volume of urethral lumen and lower lymphocyte infiltration. Volume of urethral epithelium was highest in the PDS group compared to the other operated groups. There was no significant difference regarding collagen deposition and fibroblast infiltration among the operated groups. Conclusions: The Monocryl and PDS groups showed better results.