Arthrogryposis, which represents a group of congenital disorders, includes various forms. One such form is amyoplasia, which most commonly presents in a sporadic form in addition to distal forms, among which hereditary cases may occur. This condition is characterized by limited joint mobility and muscle weakness, leading to limb deformities and various clinical manifestations. At present, the pathogenesis of this disease is not clearly understood, and its diagnosis is often complicated due to significant phenotypic diversity, which can result in delayed detection and, consequently, limited options for symptomatic treatment. In this study, a transcriptomic analysis of the affected muscles from patients diagnosed with amyoplasia was performed, and more than 2000 differentially expressed genes (DEGs) were identified. A functional analysis revealed disrupted biological processes, such as vacuole organization, cellular and aerobic respiration, regulation of mitochondrion organization, cellular adhesion, ATP synthesis, and others. The search for key nodes (hubs) in protein–protein interaction networks allowed for the identification of genes involved in mitochondrial processes.