Objective: Genetic diagnosis of muscular dystrophies (MDs) has classically been guided by clinical presentation, muscle biopsy and muscle MRI data. Muscle MRI suggests diagnosis based on the pattern of muscle fatty replacement. However, patterns overlap between different disorders and knowledge about disease-specific patterns is limited. Our aim was to develop a software-based tool that can recognize muscle MRI patterns and thus aid diagnosis of MDs. Methods: We collected 976 pelvic and lower limbs T1 weighted muscle MRIs from 10 different MDs. Fatty replacement was quantified using Mercuri score and files containing the numeric data were generated. Random forest unsupervised machine learning was applied to develop a model useful to identify the correct diagnosis. 2000 different models were generated and the one with higher accuracy was selected. A new set of 20 MRIs was used to test the accuracy of the model, and the results were compared with diagnoses proposed by 4 specialists in the field. Results: A total of 976 lower limbs MRIs from 10 different MDs were used. The best model obtained had a 95.7% accuracy, with 92.1% sensitivity and 99.4% specificity. When compared with experts on the field, the diagnostic accuracy of the model generated was significantly higher in a new set of 20 MRIs. Conclusion: Machine learning can help medical doctors in the diagnosis of muscle dystrophies by analyzing patterns of muscle fatty replacement in muscle MRI. This tool can be helpful for daily clinics but also in the interpretation of the results of next generation sequencing tests. Classification of Evidence: This study provides Class II evidence that a muscle MRI-based artificial intelligence tool accurately diagnosis muscular dystrophies.