Background: Moxibustion treatment has been found to ameliorate clinical symptoms including abdominal pain, diarrhoea and constipation in patients with irritable bowel syndrome (IBS). Herein we investigated the mechanisms underlying the use of moxibustion in a rat model of IBS. Methods: In our study, an IBS model was established in rats by colorectal distension (CRD) stimulus and mustard oil enema. The rats were randomly divided into a normal group, model group, mild moxibustion group, electroacupuncture group, probiotic group and dicetel group. Abdominal withdrawal reflex (AWR) scores were determined within 90 min of the last treatment. The expression of GDNF/GFR alpha 3 protein and mRNA in the colon and spinal cord were detected by immunohistochemistry and quantitative real-time-PCR, respectively. Results: The IBS model rats had significantly higher AWR scores than the normal group (P<0.01). After mild moxibustion treatment, the AWR score was significantly reduced (20 mm Hg, P<0.05; 40 mm Hg, 60 mm Hg and 80 mm Hg, P<0.01). The model group showed significantly more colonic glial cell line-derived neurotrophic factor (GDNF/GFR alpha 3 (GDNF family receptor alpha 3) protein and mRNA expression in the colon and spinal cord than the normal group (P<0.01). Compared with the model group, the expression of GDNF/GFR alpha 3 protein and mRNA in the colon and spinal cord of the rats were significantly decreased in the mild moxibustion group (colon: GDNF and GFR alpha 3 protein, P<0.01; GDNF and GFR alpha 3 mRNA, P<0.01; spinal cord: GDNF and GFR alpha 3 protein, P<0.01; GDNF mRNA, P<0.05, GFR alpha 3 mRNA, P<0.01). Conclusions: Our data suggest that moxibustion therapy may mitigate CRD-induced increases in the expression of GDNF and its receptor GFR alpha 3 in the colon and spinal cord in a rat model of IBS.