Nasal septal perforation (NSP) is an uncomfortable condition that usually has a negative effect on the quality of life and is frequently seen as a complication of nasal surgical procedures. The aim of this study was to evaluate the effect of allergic rhinitis (AR) on the occurence rates of septal perforation as a complication of septoplasty. The medical records of 352 patients who had septoplasty at our department between January 2006 and May 2009 were searched thoroughly and those with a follow-up period of at least 1 month were included in the study. Septal perforation rates were compared between two groups, one of which was formed by patients known to have AR besides septum deviation and the other with no history of AR. Of the 352 patients, 70 (19.8%) had accompanying AR. Only three patients (0.9%), two in the non-allergic group (NAG) and one in the allergic group (AG), were noted to have NSP after septoplasty. According to this clinical data, NSP rates were 1.4 and 0.7%, respectively, in AG and NAG. No statistical significance was found between the two groups (p = 0.487). AR had no impact on the risk of NSP after septoplasty. To our opinion, an appropriate surgical technique and a respectful approach to the tissue planes are the key points of avoiding undesired results.