Suture materials are widely used in urological surgery especially in regions that are in contact with urine. In this study, we aimed to compare polyglactine 910, cromed catgut and polydioxanone sutures according to stone formation and inflammation, congestion and foreign body reaction that occur on bladder mucosa. Cystotomy procedure was performed, in three groups of Wistar female rats, with 4/0 polyglactine 910, 4/0 chromed catgut and 4/0 polydioxanone sutures. All groups were divided into two sub-groups with 4 and 8-week follow up periods. Rats were treated with 20 mg kg−1 day−1 Ofloxacin (i.p.) daily until the seventh post-operative day. Urinary pH, leucocyte esterase and nitrite levels were determined. All rats were killed at the end of the follow-up period and stone formation on sutures and degrees of tissue reactions (inflammation, congestion and foreign body reaction) on bladder mucosa were compared. Tissue reactions were evaluated by the same pathologist (S. K.). Chi-square and Student’s t test were used in statistical analysis (p < 0.05). There was no significant difference between the mean weights of the groups. Leucocyte esterase and nitrite were negative in urine analyses. There was no significant difference between urinary pH levels of the groups with 4 and 8 weeks follow-up (p > 0.05). Although the difference between the degrees of congestion in groups was not statistically significant (p > 0.05), there were statistically significant differences between the degrees of inflammation and foreign body reaction in groups. Although the duration of urinary contact of suture is the main factor in stone formation on suture material, tissue reaction on mucosa and the physical structure of suture also affect this formation. We observed lower degrees of inflammation and foreign body reaction with 4/0 polydioxanone and no stone formation. We believe that polydioxanone may be useful and reliable in urological surgery due to these properties.