The clinical features of myotonic dystrophy type 1 (DM1) and type 2 (DM2) may present striking similarity, whereas, in some cases, the DM2 phenotype may be so mild that the diagnosis may be missed. Therefore, the identification of disease-specific histopathological patterns for DM1 and DM2 may help clinicians to correctly address genetic studies. We performed a comparative morphological and morphometric analysis on muscle biopsies from 10 DM1 and 11 DM2 patients, comparing type 1 and type 2 fibers as to: fiber type predominance, transverse diameter, atrophy and hypertrophy factors, and prevalence of central nuclei. In DM1 cases we observed preferential type 1 fiber atrophy and a higher prevalence of central nucleation among type 1 fibers in all cases. In DM2 muscle biopsies, high rates of atrophic and hypertrophic type 2 fibers were observed in most cases, and preferential central nucleation in type 2 fibers was present in all cases. As opposed to DM1, in which type 1 fibers display most of the histological changes, preferential atrophy and hypertrophy of type 2 fibers may be considered as markers of DM2. A higher prevalence of central nuclei among hypertrophic type 2 fibers has a predictive value for the diagnosis of DM2. Thus, morphometric and fiber type-based histological analysis of muscle biopsies may help differentiate between DM1 and DM2 and guide molecular analysis.