Objective The purpose of this study was to examine the effects of pulsing electromagnetic field and calcitonin gene related peptide on colostomy induced colonic atrophy in rat. Methods Rats undergoing diverting colostomy with exclusion of distal colon received the stimulation of pulsing electromagnetic field or sham stimulation in a special device 30 min/day for consecutive five days. Results Electromagnetic stimulation significantly prevented the colonic atrophy, and elevated the colonic mucosal DNA and RNA contents compared to those without stimulation. Diverting colostomy reduced the concentration of calcitonin gene related peptide in serum, on which the application of electromagnetic stimulation had no effect. Conclusion Pulsing electromagnetic field prevents surgically induced intestinal mucosal atrophy. This stimulation does not change the concentration of calcitonin gene related peptide indicating the complexity of the mechanism of mucosal atrophy.