Some conventional and quantitative EMG studies have already demonstrated a subclinical lower motor neuron involvement in juvenile myoclonic epilepsy (JME). Our aim was to investigate this subclinical involvement by using motor unit number estimation (MUNE) analysis with modified McComas' technique. We enrolled 75 consecutive JME patients and 26 normal controls. All subjects underwent motor and sensory nerve conduction studies, concentric needle EMG and MUNE analysis of the M. abductor pollicis brevis (APB) and M. tibialis anterior (TA). The clinical and EEG findings were evaluated to correlate with MUNE values. MUNE values of the APB (54+/-25) and TA (35+/-17) muscles were significantly lower in the JME group (p<0.001) when compared to the normal controls (109+/-24 and 80+/-26 for APB and TA muscles, respectively). Our findings show that anterior hom cells were subclinically affected in some JME patients, suggesting a shared background for both JME phenotype and grey matter disorganization in spinal cord.