The effects of chronic exposure (2 h daily for 21 days) of 1 kHz square wave-modulated 2450 MHz microwave radiation (non-thermal) on sleep-EEG, open field behavior, and thyroid hormones (T(3), T(4), and TSH) have been analyzed in an animal model. Results revealed significant changes in these pathophysiological parameters (p < 0.05 or better), except body temperature, grooming behavior, and TSH levels. The sleep-EEG power spectrum data for slow wave sleep (SWS), rapid eye movement (REM) sleep, and awake (AWA) states in two experimental groups of rats (microwave exposed and the control) were tested by an artificial neural network (ANN), containing 60 nodes in input layer, weighted from power spectrum data from 0 to 30 Hz, 18 nodes in hidden layer and an output node. The target output values for this network were determined with another five-layered neural network (with the structure of 6-14-1-14-6). The input and output of this network was assigned with the six confirmed pathophysiological changes. The most important feature for chronic exposure of 2450 MHz microwave exposure and for control subjects was extracted from the third layer single neuron and used as the target value for the three-layered ANN. The network was found effective in recognizing the EEG power spectra with an average of 71.93% for microwave exposure and 93.13% for control subjects, respectively. However, the lower percentage of pattern identification agreement in the microwave-exposed group in comparison to the control group suggest only mild effects of microwave exposure with this experimental setup.