Noise exposure is one of the most common causes of hearing loss. There is growing evidence suggesting that noise-induced peripheral hearing loss can also induce functional changes in the central auditory system. However, the physiological and biological changes in the central auditory system induced by noise exposure are poorly understood. To address these issues, neurophysiological recordings were made from the auditory cortex (AC) of awake rats using chronically implanted electrodes before and after acoustic overstimulation. In addition, focused gene microarrays and quantitative real-time polymerase chain reaction were used to identify changes in gene expression in the AC. Monaural noise exposure (120 dB sound pressure level, 1 h) significantly elevated hearing threshold on the exposed ear and induced a transient enhancement on the AC response amplitude 4 h after the noise exposure recorded from the unexposed ear. This increase of the cortical neural response amplitude was associated with an upregulation of genes encoding heat shock protein (HSP) 27 kDa and 70 kDa after several hours of the noise exposure. These results suggest that noise exposure can induce a fast physiological change in the AC which may be related to the changes of HSP expressions.