The alpha-actinins belong to a superfamily of cytoskeletal proteins, and their role in human genetic diseases is still unclear. Therefore, they could be good candidates for muscular dystrophies of unknown etiology. We have analyzed alpha-actinin-3 (ACTN3) in muscle biopsies from a total of 54 patients. A complete deficiency was found in 9 patients: 2/12 with classical merosin-positive congenital MD (CMD), 1/12 with Severe Childhood Autosomal Recessive MD (DLMD), but with a positive IF pattern for the proteins of the sarcoglycan complex: 3/14 with mild limb-girdie MD (1LGMD2A and 2 yet unclassified), 1/10 with sarcoglycanopathies (LGMD2C), and 2/6 with Xp21 Duchenne MD (DMD). Patients within the same family, and with the same disease (DMD, LGMD2A, LGMD2C), were discordant for ACTN3 deficiency. Additionally, no correlation was found with the degree of muscle degeneration, nor with the clinical course. One ACTN3-deficient CMD patient showed no mRNA expression for the muscle ACTN3 gene, but the other ACTN3-deficient patients with different forms of muscular dystrophy showed very low or no mRNA expression as well. These results show that the deficiency of ACTN3 is a secondary effect in these dystrophies.