This study was designed to assess the effects of raising mucoperiosteal flaps and exposing palatal bone at the time of palatoplasty. Using 62 beagle puppies as subjects, we tested the hypothesis that raising mucoperiosteal flaps does not interfere with craniofacial growth. We further hypothesized that the size of the area of bone exposed following palatoplasty does affect subsequent craniofacial growth. The animals were divided into four groups: two control groups (unoperated and unrepaired) and two experimental groups. In the first experimental group, two-flap palatoplasty was used to close the surgically induced palatal defect, leaving narrow strips (0 to 2.5 mm) of bone exposed lateral to the flaps. In the second group, one flap was raised to close the defect, leaving a wide area (5 to 6 mm) of palatal bone exposed on one side. Thirty-four direct craniometric measurements were analyzed. Animals that had elevation of both mucoperiosteal flaps with narrow strips of denuded bone on both sides had less severe craniofacial growth aberrations than those in which the defect was left unrepaired or was repaired with one mucoperiosteal flap leaving a wider area of bare bone exposed. These findings suggest that raising mucoperiosteal flaps is less detrimental to craniofacial growth than leaving large areas of exposed palatal bone.