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We report a case of middle cerebral artery stroke with heterozygosity for 2 separate hypercoagulable conditions following repair of an H-type tracheoesophageal fistula (TEF) in an infant. Neonatal stroke is rare, occurring in 1 in 4000 births annually in the United States. Stroke after pediatric surgery occurs in approximately 0.05% of patients. Etiologies of stroke in neonates include cardiac, hematologic, vascular, traumatic, metabolic, pharmacologic, infectious, and hypoxemic insults. Thrombophilia has been described in 42% to 78% of neonates with neonatal stroke. Stroke after repair of an H-type TEF has not been reported as a postoperative complication. Manipulation of the carotid artery during this operation is presumed to have contributed to a thromboembolic event in this infant with a hypercoagulable state. Whereas preoperative workup may not be indicated due to the low prevalence of neonatal stroke, workup for a congenital hypercoaguable condition may be considered in infants with stroke as a postoperative complication. This report provides a concise review of the etiology and treatment of stroke and hypercoagulable states in neonates as well as presents the case of a previously undescribed complication of repair of an H-type TEF.