Aplasia of major salivary glands is a rare disorder with only a handful of cases reported in the literature. The cause of congenital absence of the salivary glands has not been determined, but it may be associated with ectodermal defects of the first and second branchial arches. Patients may be asymptomatic or may experience dysphagia, xerostomia, several periodontal disease, or multiple caries. There are few reports of patients with congenital gland aplasia with cleft lip and palate. We document the case of a 41-year-old patient with repaired unilateral cleft lip palate, bilateral submandibular gland aplasia, and compensatory hypertrophy of the sublingual glands. To the best of our knowledge, there are no previous reports that can be found in the literature with a combination of such findings.