Background: The purpose of this study was to evaluate the association between the use of relaxing incisions and maxillary growth disturbance after primary palatoplasty in patients with unilateral cleft lip and palate. Methods: This is a prospective, randomized, double-blind controlled trial study with ethical committee approval between 2 groups of patients with unilateral cleft lip and palate who were operated on using the two-flap and one-flap techniques from 2008 to 2011. Two groups of patients with unilateral cleft lip and palate were operated on using the mentioned techniques by the Outreach Surgical Center Program Lima since 2008. Data collection was accomplished by evaluation of maxillary arch dimensions and dental arch relationships (scored using the 5-year-olds' index). Results: The mean score for the 5-year-olds' index was 2.57 for two-flap technique and 2.80 for one-flap technique without statistical significant differences (P = 0.71). Our comparative study did not find statistically significant differences in maxillary arch dimensions between the studied techniques for unilateral cleft palate repair. Good levels of agreement were observed according to the ê statistics. Conclusions: The results arising from this clinical trial do not provide statistical evidence that one technique let us obtain better maxillary development than the other at 5 years. The use of relaxing incisions was not associated with maxillary growth impairment. A technique with limited relaxing incisions does not has better maxillary growth. Additional longer term study is necessary to confirm this preliminary report.