Involuntary movements such as levodopa-induced dyskinesia in Parkinson's disease (PD) and chorea in Huntington's disease (HD) are the consequence of two distinct basal ganglia dysfunctions. Yet, their clinical manifestations seem to resemble each other. We seek to determine how to detect PD dyskinesia and HD chorea during quiet stance using healthy control subjects' postural sway as a base measure and identify means to distinguish mathematically HD chorea from PD dyskinesia. Movements were recorded using a magnetic tracker system with fifteen sensors placed strategically to capture whole-body displacement. Choreic and dyskinetic patients as well as healthy controls were asked to stand with arms stretched horizontally in front of them for 60 s. We examined amplitude, frequency dispersion, proportional energy, sample entropy, kurtosis, skewness, amplitude fluctuation, maximum coherency between 44 pairs of body segments. The choreic and dyskinetic movements revealed similar patterns of sample entropy, amplitude fluctuation, and coherencies between body segments. However, skewness and kurtosis for velocity of movements were found to be higher in HD chorea than in PD dyskinesia, reflecting rapid movements in HD patients. There was also a tendency for the frequency composition of PD dyskinesia to be more concentrated in the 1.0-1.5 Hz range. Our results show that despite their similarities in apparent randomness and lack of coordination, dyskinesia associated with treatment of PD and chorea in HD each have their own distinctive characteristics which may be related to their specific pathophysiology.