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Muscle magnetic resonance imaging (MRI) and ultrasound (US) are emerging tools to assist in the diagnosis of children with genetic muscle disease. Increasing number of studies demonstrate that these imaging techniques can identify selective patterns of muscle atrophy, fatty degeneration, and muscle edema that help to distinguish between different early-onset genetic myopathies and muscular dystrophies. Recognizing patterns of pathology by muscle imaging can help to guide genetic testing and avoid the more invasive procedure of a muscle biopsy. Conversely, since massive parallel sequencing is now more commonly used as the initial step in diagnostic testing, imaging techniques can help to confirm or exclude if a variant of uncertain significance is indeed disease causing and compatible with a pattern of pathology as detected by muscle imaging. Whereas for diagnostic purposes and pattern recognition, muscle pathology does not need to be quantified, measuring disease progression is increasingly supported by quantitative muscle imaging, which is critical given the recent increment in rare disease therapeutic trials. Here, we discuss the value of muscle imaging techniques in pediatric muscle disease and summarize data identifying specific patterns of involvement in muscle MRI and US in some of the more common genetic myopathies and muscular dystrophies.