Healthy muscle relies on a complex and interdependent network that includes, but is not limited to, proteins, ion channels, and the production and utilization of ATP. Disruptions to the system can occur for a number of reasons (genetic mutations, toxins, systemic disease, inflammation), yet they clinically present with symptoms that are nonspecific and common to myopathies: weakness, muscle pain, cramping, hypotonia. This article uses a case-based format to review the clinical reasoning and diagnostic tools that guide the accurate diagnosis of myopathies. We specifically focus on toxic, metabolic, mitochondrial, and late-onset congenital myopathies.