An algorithm that generates electromyographic (EMG) signals consistent with those acquired in a clinical setting is described. Signals are generated using a model constructed to closely resemble the physiology and morphology of skeletal muscle, combined with line source models of commonly used needle electrodes positioned in a way consistent with clinical studies. The validity of the simulation routines is demonstrated by comparing values of statistics calculated from simulated signals with those from clinical EMG studies of normal subjects. The simulated EMG signals may be used to explore the relationships between muscle structure and activation and clinically acquired EMG signals. The effects of motor unit (MU) morphology, activation, and neuromuscular junction activity on acquired signals can be analyzed at the fiber, MU and muscle level. Relationships between quantitative features of EMG signals and muscle structure and activation are discussed.