OBJECTIVE Although classic and occult submucous clefts have been well described with respect to clinical features and endoscopic findings, there is a paucity of information regarding the histologic characteristics of the midline palatal area and its role in the clefting process. This preliminary study describes the histopathologic features of classic and occult submucosal clefts. METHODS Twenty-eight patients with classic submucous cleft (12 patients) and occult submucous cleft (16 patients) were available for study. Histopathologic evaluation of two biopsies from each patient (muscular uvulae biopsy; levator muscle bundle biopsy) was performed. RESULTS Submucosal fibrosis with relatively dense collagen deposition was noted in both the musculus uvulae and levator muscle bundle biopsy sites. Individual myocytes and myocyte fascicles were entrapped and encased by fibrotic tissue, resulting in disruption of the fascicular organization. Most fascicles were disrupted by intervening dense collagen bands within and interposed between the fascicles. The myocytes had an atrophic or hypoplastic appearance with cross-sectional diameters ranging from 42% to 61% (mean reduction, 53%) less than those expected for myocytes from normal palates. There was fascicular disorganization with intermixing of longitudinally and cross-sectionally oriented myocyte groups. Minor salivary glands were affected as well with increased collagen deposition between and within lobules of salivary gland tissue. CONCLUSIONS This histopathologic study indicates that significant fibrosis is present within submucosal cleft regions and is associated with myocyte atrophy or hypoplasia. The relatively dense fibrosis appears to be a well-organized, chronic process and is present in the absence of significant chronic inflammation. In addition, there is myocyte fascicular disorganization with a haphazard arrangement. This disorderly arrangement may imply that there is a failure of resorption of the epithelial/mesenchymal tissue during palatine shelf closure with retention of mesenchymal tissue that contains the insertion of the velopharyngeal musculature apparatus.