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Background: Stomatitis is a disturbing side-effect of chemotherapy that disturbs patients and causes difficulties in patient’s drinking, eating and talking, and may results in infection and bleeding. Objectives: This study aimed to investigate the effect of Yarrow distillate in the treatment of chemotherapy-induced stomatitis. Patients and Methods: This randomized controlled trial study was conducted during 2013. The study population consisted of all cancer patients with chemotherapy-induced oral stomatitis referred to Shahid Beheshti Medical Center, Kashan, Iran. The data collection instrument had two-part; a demographic part and another part recording the severity of the stomatitis at the first, seventh, and 14th days of the intervention based on a WHO criteria checklist in 2005. In this study, 56 patients diagnosed with cancer were randomly assigned into control and experimental groups in similar blocks according to their stomatitis severity. The experimental group gargled 15 mL of a routine solution mixed with Yarrow distillate 4 times a day for 14 days while the control group gargled 15 mL of routine solution. The severity of stomatitis was assessed at the beginning of the intervention, and then after 7 and 14 days of the study. Data were analyzed using chi-square and Fisher exact test, Mann-Whitney U, Kruskal-Wallis, and Friedman tests using SPSS 11.5 software. Results: At first, the median score of stomatitis in the experimental group was 2.50 that significantly reduced to 1 and 0 in days 7 and 14 of the intervention, respectively ( P value < 0.001). However, in the control group, the median score of stomatitis was 2.50, which significantly increased to 3 in days 7 and 14 ( P value < 0.001). Conclusions: Yarrow distillate-contained solution reduced stomatitis severity more than the routine solution. Therefore, we suggest using it in patients with chemotherapy-induced stomatitis.