Congenital muscular dystrophies (CMDs) are a genetically heterogeneous group of neuromuscular disorders that include a wide spectrum of clinical and pathological features. Mutations in several genes that encode extracellular matrix, nuclear envelope, sarcolemmal proteins and glycosylation enzymes are known to be responsible for CMDs. The large overlap of clinical presentations resulting from different gene mutations poses a challenge for clinicians in determining disease etiology for each patient. The aim of this study was to investigate the use of whole exome sequencing (WES) to identify the causative gene(s) in three CMD families with similar clinical features, including early-onset generalized weakness, severely elevated serum CPK levels, and rapid progression of disease. The highly consanguineous first family had two affected children diagnosed with CMD at the age of 1.5 years. Serum CK levels in the older sibling were 728 and 4909 IU/L at 2 and 6 years. WES of DNA from one affected child identified a known homozygous frameshift mutation in the dysferlin gene ( DYSF ): c.2779delG, p.A927LfsX21 in the patient. Reexamination of patient muscle biopsy in light of the genetic findings revealed absence of dysferlin protein. The second family had one affected child with CK levels of 2675 and 4025 IU/L at 1.5 and 3 years. WES revealed compound heterozygous missense mutations in the fukutin ( FKTN ) gene: a novel mutation (c.G915C, p.W305C) and a known mutation (c.G920A, p.R307Q) in the patient. All known muscle disease genes were excluded by WES in one affected individual from the third family with two affected children. Studies are ongoing for identifying the causative gene in this family. Our results highlight the genetic heterogeneity in patients diagnosed with CMD and suggest that WES may represent a powerful diagnostic tool for neuromuscular diseases with shared clinical and pathological presentations.