Background: Allergic rhinitis is the most common type of allergic disease among population. Its accurate treatment is very important for cutting of allergic march. On the other hand, gasteroesophageal reflux disease (GERD) is one of the most common gastrointestinal problems among allergic patients mainly asthmatic cases. It might conflict treatment. Despite of asthma, a few studies have been conducted on the impact of GERD treatment on allergic rhinitis symptoms. In this study, we assessed GERD treatment and its effects on improving of allergic rhinitis patients with GERD. Materials and Methods: In a prospective cross-sectional study, March - September 2012, 103 consecutive patients with persistent moderate to severe seasonal allergic rhinitis enrolled. For allergic rhinitis patients with GERD 20 mg omeperazole once daily for 6 weeks prescribed, empirically. Conventional allergy treatment continued and finally the allergic rhinitis symptoms were assessed clinically and recorded before, 5th, 10th and 30th days of omeprazole treatment period. Results: Our study included 103 patients with seasonal allergic rhinitis who were divided into GERD (n=33, 38%) and non-GERD (n=70, 68%) groups with the mean age 28 and 25.7 years, respectively. The first group developed significant improvement for GERD symptoms on days 5, 10 and 30 after beginning of therapy (P=0.03). No association was found between GERD treatment and relief of allergic symptoms or TNSS improvement (P>0.05). Data analyzed by Epi info (ver 7) and SPSS software (ver 11.5), and by Chi squeare test and paired T test. P lower than 0.05 was considered as significant. Conclusion: This study showed no significant association between empirical treatment of GERD and improvement of allergic symptoms in patients with allergic rhinitis. However, further studies with a larger sample size might be needed.