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We describe a surgical method for ileal resection and anastomosis in newborn germfree piglets that was undertaken to establish a model that can be used for immunologic research and other applications. A preliminary experiment indicated that neonatal piglets with resection of approximately 60 cm of their ileum (removal of approximately 90% of the continuous ileal Peyer patches; group A) and those in which the ileum was transected (group B) could be maintained germfree for 35 d, colonized with defined gut flora, and maintained in a clean room until 70 d of age. In the final study, 12 piglets (4 each for groups A and B and 4 untreated controls), were monitored for postoperative feeding behavior, malaise, evidence for contamination with pathogenic bacteria, and weight gain. All surgical animals were free from incidental contamination from pathogens and environmental organisms with atypical colony types for 35 d. Two piglets in group B died postoperatively (1 during the preliminary experiment and 1 during the final study). Control (group C) piglets gained significantly more weight than did those in group A. These studies demonstrated that surgical resection of the ileal Peyer patches under germfree conditions can be accomplished successfully without compromising piglet health or introducing pathogens and with only a modest reduction in weight gain.