Background: Spinal muscular atrophy includes a group of neuromuscular disorders characterized by degeneration of anterior horn cells in the spinal cord, and leads to progressive muscular weakness. NAIP is one of the genes that inhibits motor neuron apoptosis. Deletion of this gene is usually observed in type I SMI. The aim of this study was to investigate the frequency and pathogenicity of NAIP gene among SMA patients in east Azerbaijan and neighboring regions within the years 2004-2005. Materials and Methods: This descriptive study was carried out on 50 patients suffering from SMA by extracting DNA and molecular genetic survey of the samples. Exons 5 and 13 of NAIP gene and microsatellite D5S1416 were amplified using polymerase chain reaction (PCR) and the product on agar gel and polyacrylamid gel was put on electrophoresis through ethidium bromide stain and silver nitrate stain respectively and the frequency of different types of SMA with NAIP gene deletion was calculated. To determine the relation between gender and disease intensity test was used. Results: Out of 50 SMA patients 28% showed deletion in NAIP gene all belonging to type I of the disease with the highest disease intensity. Nine patients (64%) with deleted NAIP gene were the outcome of consanguineous marriage. Disease intensity in type I patients lacking NAIP gene was higher than type I patients with healthy genes. Conclusion: In 28 percent of patients NAIP deletion was observed. Consanguineous marriage is a promoting factor in gene mutation purification and birth of diseased neonates in studied samples. It is recommended that the families with SMA background refer to molecular genetic centers for prenatal diagnosis and close relatives avoid consanguineous marriage.