The association between survivor motor neuron (SMN) gene deletions and motor neuron diseases such as spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS) suggest that sporadic lower motor neuron disease (LMND) may be related to SMN gene deletion. We examined the association between copy numbers of SMN and the risk of LMND among Koreans. We genotyped the copy number of SMN1 and SMN2 in 18 patients diagnosed with sporadic LMND and 100 neurologically healthy subjects using the multiplex ligation-dependent probe amplification (MLPA) method. A total of eight SMN1:SMN2 genotypes (1:1, 1:3, 2:0, 2:1, 2:2, 2:3, 3:2, and 2:2/3:1 of exon7/exon8) were found. We found that homozygous deletion of SMN2 was significantly related to LMND (OR 20.7; 95% CI 2.8-150.5; p = 0.003). There was no significant difference in the distribution of the SMN1 copy number between the LMND patients and controls. In contrast to ALS, the risk of which is influenced by various factors other than SMN copy number itself, the association studies in LMND show a consistent finding that homozygous deletion of SMN2 may be specifically related to LMND, despite the small number of subjects.