Limb-girdle muscular dystrophy 1F (LGMD1F) is an autosomal dominant muscular disease affecting a Spanish family. Using whole genome sequencing, we identified a single nucleotide deletion (c.2771del) in transportin-3 gene (TNPO3) in a LGMD1F patient. The mutation disrupts the termination codon of TNPO3 and causes a reading frame shift. Transportin-3 is a nuclear protein, and mediates import of serine–arginine rich proteins into nucleus, which is important for mRNA splicing. This study aimed to investigate the significance of transportin-3 in the pathogenesis of LGMD1F.We performed dideoxy-sequencing of TNPO3 in 24 affected and 23 unaffected family members. Muscle specimens from 4 patients were analyzed by conventional stains and immunohistochemistry. Direct sequence of TNPO3 revealed that all patients carried a heterozygous mutation, and none of the unaffected subjects had the mutation. Hematoxylin-eosin (HE) stained muscle revealed nuclei (10.7±3.0%; mean±SD) with central pallor in all patients studied. Immunohistochemistry with anti-transportin-3 antibody showed colocalization with nuclei in control subjects. In patients, transportin-3 was also observed within nuclei, but was often unevenly distributed in periphery, a staining pattern similar to that seen by HE. Genetic and histological studies in a Spanish family strongly support the hypothesis that TNPO3 is the causative gene of LGMD1F. Pathological study also indicates that the subcellular distribution of transportin-3 is disrupted and affects the structure of nuclei.