The brain derived neurotrophic factor (BDNF) val66 met polymorphism affects function of the motor system in young subjects, but little is known about motor system effects in the elderly. The current study assessed motor system physiology and behavior, plus a measure of short-term motor cortex plasticity using transcranial magnetic stimulation, in 38 elderly subjects, then examined whether findings varied in relation to BDNF genotype. Baseline data were also collected from 14 young subjects. At baseline, elderly subjects had poorer motor performances, larger motor cortex maps, and smaller motor evoked potentials compared to young subjects. Degree of age-related differences in neurophysiology correlated inversely with motor performance, for example, larger map area correlated with weaker pinch grip force (r= −0.42, P=0.01). In elderly subjects, baseline behavior and neurophysiology did not differ in relation to BDNF genotype. In addition, although map area increased significantly (P=0.03) across 30 minutes of exercise, this change did not vary according to BDNF genotype. Aging is associated with changes in neurophysiology that might represent a compensatory response. The data do not support an association between BDNF genotype and behavior, neurophysiology, or short-term cortical plasticity in the motor system of healthy elderly subjects.