Background The Peruvian health system is limited in providing specialized care for patients with clefts because there are an insufficient number of hospitals and few specially trained doctors in rural areas of the country. The most common model of care in these areas is the surgical mission wherein experienced cleft surgeons perform surgeries and teach local doctors. The purpose of this research was to identify the differences in outcome between the surgical mission trip and the referral center model of care provided by the same team. Methods A retrospective analysis (2002-2012) was performed on data from surgical outcomes provided by the Outreach Surgical Center Lima that utilized both models of care (surgical mission and referral center).Atotal of 935 procedures were performed in 680 patientswith clefts whowere treated by the Outreach Surgical Center Program Lima since 2002. atients in both groups were identified from our records (medical records and screening-day registries). All patients underwent a physical examination, had photographs taken, and any unfavorable results and complications were documented. omparison of categorical variables (including outcomes) between caremodels was performed using Pearson's v2 test or Fisher's exact test when appropriate. In all cases a two-tailed test was performed and the p value for rejecting the null hypothesis (no difference or no association) was set at 0.05. esults We found significant differences between the two models of care with respect to unilateral cleft lip and cleft palate dehiscence (p = 0.02 and p = 0.04, respectively), palate postoperative hemorrhage (p < 0.01), and palatal fistula (p < 0.01) outcomes. Discussion Differences in observed surgical outcomes between the two models might be attributed to the surgeon's performance and/or the patient's age, and these factors are also considered with respect to the model of care. Limitations in long-term medical evaluation at each site should be identified and strategies to improve surgical outcomes must be developed to ensure that patients served by surgical missions obtain the same results achieved at a referral center.