Rationale and Objectives: To confirm the feasibility and compare the accuracy of magnetic resonance imaging intravoxel incoherent motion (IVIM) and T2 mapping models for the differentiation of autoimmune myositis from muscular dystrophy. Materials and Methods: Fourty-two autoimmune myositis and 11 muscular dystrophy patients proven by diagnostic criteria were enrolled in the study. Conventional MR sequences, IVIM, and T2 mapping through the bilateral thighs were obtained as well as blood samples for all patients. IVIM and T2 mapping parameters as well as serum markers were compared between the autoimmune myositis and muscular dystrophy groups. Mann-Whitney U tests were performed for statistical analysis along with receiver operating characteristic curves. Spearman correlation coefficient models were constructed to analyze the correlation between IVIM and T2 mapping with serological parameters. Results: The intramuscular apparent diffusion coefficient, tissue diffusivity (D), perfusion fraction (fp), and T2 relaxation time values were statistically significantly different between the autoimmune myositis and muscular dystrophy groups (p < 0.05). Pseudo diffusivity (Dp) values showed no statistical difference between the groups (p > 0.05). D parameter of IVIM sequences differentiated autoimmune and muscular dystrophy with a higher specificity of 75.60%. T2 values within the thighs were correlated with serum creatine kinase and lactate dehydrogenase levels (p < 0.05). Conclusion: Thigh muscle IVIM and T2 mapping parameters are useful in differentiating autoimmune myositis from muscular dystrophy, particularly the IVIM parameters.