This paper describes the results of continuous, three-year treatment of Duchenne muscular dystrophy (DMD) patients with eteplirsen, 30 nucleotide-long phosphorodiamidate morpholino oligomer (PMO) designed to skip DMD exon 51 in patients with DMD. Progression of eteplirsen-treated patients ≥7 years was compared to matched historical controls (HC). The primary functional assessment in this study was the 6-Minute Walk Test (6MWT). Respiratory muscle function was assessed by pulmonary function testing (PFT). Longitudinal natural history data were used for comparative analysis of 6MWT performance at baseline and Months 12, 24, and 36. Patients were matched to the eteplirsen group based on age, corticosteroid use and genotype. At 36 months, eteplirsen-treated patients (N=12) demonstrated a statistically significant advantage of 151 meters (p<0.01) on 6MWT and experienced a lower incidence of loss of ambulation in comparison to matched HC (N=13) amenable to exon 51 skipping. PFT results remained relatively stable in eteplirsen-treated patients. Eteplirsen was well-tolerated. Analysis of HC confirmed the previously observed change in disease trajectory at age 7, and more severe progression was observed in patients with mutations amenable to exon skipping than in those not amenable. The sub-set of patients amenable to exon 51 skipping showed a more severe disease course than those amenable to any exon skipping