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Background: This study aimed to survey the use of complementary and alternative medicine (CAM) therapies in Japanese children with major pediatric surgical diseases. Methods: This survey was mailed to each family of 355 patients. Results: One hundred fifty-three (43%) of 355 mailed questionnaires were completely returned. Forty-one (27%) of 153 parents responded that they used CAM for their child. There was no significant difference in CAM use according to sex, mean age, follow-up duration, family CAM users, and associated disorders between CAM users and non-users. Children with inflammatory bowel disease (IBD) were significantly more likely to use CAM than children without IBD (65% vs 21%, p = 0.0001). Only 20% of parents informed the attending physicians about CAM before its use. Conclusions: It is important for physicians caring for children with pediatric surgical disease, especially IBD, to be familiar with common forms of CAM.