Congenital heart defects and skeletal malformations syndrome (CHDSKM; OMIM #617602) is a rare syndrome characterized by distinctive facial features, congenital cardiac lesions, failure to thrive, and skeletal abnormalities. Hearing impairment, renal, and ophthalmological abnormalities have also recently been reported. We report here the clinical and molecular phenotype of an adolescent male who presented with multisystem involvement suggestive of a connective tissue disorder. The proband presented with the typical dysmorphic, skeletal, and skin findings of CHDSKM. In addition, he had several features not previously documented, including severe and rapidly progressive aortic root dilatation as well gastro-intestinal reflux secondary to esophageal dysmotility with gastric strictures. Genetic testing revealed a recurrent variant in the ABL1 gene, c.1066G>A, p.Ala356Thr. These novel features contribute to the growing body of knowledge regarding this rare and recently described condition as well as lend strength to previous calls for close surveillance of the aortic root from a young age in CHDSKM.