To assess the effect of two palatoplasty procedures, modified Furlow's palatoplasty (F procedure) and modified two-flap palatoplasty (T procedure), on the maxillofacial morphology of unilateral cleft lip and palate (UCLP) and bilateral cleft lip and palate (BCLP) during the primary dentition period. Retrospective cohort study. Department of Orthodontics, School of Dentistry, Showa University. We enrolled 106 pediatric patients (63 boys, 43 girls; aged 4.43 ± 0.34 years) with non-syndromic orofacial clefts who underwent cheiloplasty and palatoplasty. Patients were divided into four groups according to cleft type (BCLP or UCLP) and palatoplasty procedure type (F or T procedure). Maxillofacial morphology was assessed by examining parameters on lateral cephalograms. Multiple comparisons revealed significant differences among N-A, N-ANS, and ANS-PNS distances and SNA and ANB angles among the groups. There were significant differences in N-A, N-ANS, ANS-PNS, SNA, and SNB among the UCLP and BCLP groups. The calculated effect sizes were all within 0.3-0.5. The statistical power was as follows: N-A, 86.41%; N-ANS, 79.77%; ANS-PNS, 97.49%; SNA, 96.88%; and ANB, 99.25%. Although UCLP and BCLP both exhibited differences in craniofacial distances and angles, the procedure type (either F or T procedure) had no significant effect on the maxillofacial morphology (as determined by lateral cephalograms). However, to rule out additional bias, patient-specific factors should be considered that may be affected by maxillofacial development when deciding surgical approaches.