Background. Neonates with complex congenital cardiac lesions are largely inadequately managed in Guatemala. Methods. Between 1997 and 2009, 79 patients who underwent operations for transposition of the great arteries were identified; 51 (63.3%) had an arterial switch operation (ASO) and 28 (36%) an atrial switch operation (ATSO). The Aristotle Basic Complexity score (ABC score) and the Aristotle Comprehensive Complexity score (ACC score) have been used to aid in the evaluation of quality of care associated with pediatric cardiac surgery by adjusting for operative complexity. Results. In-hospital mortality was 47% for the ASO and 25% for the ATSO group; 36.7% were beyond 1 month of age and many exhibited increased preoperative risk factors. The mean ABC score was 9.75 ± 0.89 and the ACC score was 12.12 ± 2.7, with a mean 2.36-point increase (P < .05). Comparing survivors and nonsurvivors with both scores, significant differences were identified (ABC: P < .04 and ACC: P < .02). Conclusion. During this 13-year period, a low volume of surgery for transposition of the great arteries (TGA) was performed at our institution with a relatively high surgical mortality. Many patients with TGA in Guatemala are either never referred for surgery or referred late. Strategies to improve outcomes for neonates with TGA in Guatemala must include increases in early diagnosis countrywide and prompt referral to our unit. Based on the larger number of neonates with TGA that would be referred to our center, we anticipate that this strategy should substantially improve surgical outcomes and favor overall team-related skills.