Needle Electromyography, in combination with nerve conduction studies, is the gold standard methodology for assessing the neurophysiologic effects of neuromuscular diseases. Muscle categorization is typically based on visual and auditory assessment of the morphology and activation patterns of its constituent motor units. A procedure which is highly dependent on the skills and level of experience of the examiner. This motivates the development of automated or semi-automated categorization techniques. This paper describes a 2-stage Gaussian mixture model based approach. In the first stage, a muscle is classified as neurogenic or myopathic. The second stage uses a classifier specific to each disease category to confirm or refute the disease involvement. A total of 2556 motor unit potentials sampled from 48 normal, 30 neurogenic and 20 myopathic tibialis anterior muscles were utilized for this study. The proposed approach showed an average accuracy of 91.25%, which is higher than the compared linear and non-linear multi-class schemas. In addition to improved accuracy, the 2-stage approach is more suitable for the muscle categorization, because it has a hierarchical decision structure similar to current clinical practice, and its output can be interpreted as a measure of confidence.