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Background: To examine occurrence of cow's milk protein intolerance (CMPI) in newborns that underwent small intestine surgery and the clinical profiles of those newborns with postoperative CMPI, and to evaluate the preventive effects of probiotics on CMPI. Methods: We retrospectively reviewed from 2000 to 2009, a total of 30 newborns required surgery on their small intestines. All of these patients had received antibiotics to prevent postoperative infection. Since 2005 we adopted a protocol of targeted probiotic therapy prophylaxis. Results: Eighteen patients received probiotic therapy, while twelve did not. One infant among those eighteen patients and eight patients among those twelve developed CMPI, a significantly lower rate for the group with probiotic therapy than that without it (p