The goal of this study is to investigate functional connectivity between different brain regions by analyzing the temporal relationship of the maxima of gamma waves recorded in multiple brain areas. Local field potentials were recorded from motor cortex, hippocampus, entorhinal cortex and piriform cortex of rats. Gamma activity was filtered and separated into two bands; high (65-90Hz) and low (30-55Hz) gamma. Maxima for gamma activity waves were detected and functional connectivity between different brain regions was determined using Shannon entropy for perievent histograms for each pair channels. Significant Shannon entropy values were reported as connectivity factors. We defined a connectivity matrix based the connectivity factors between different regions. We found that maxima of low and high frequency gamma occur in strong temporal relationship between some brain areas, indicating the existence of functional connections between these areas. The spatial pattern of functional connections between brain areas was different for slow wave sleep and waking states. However for each behavioral state in the same animal the pattern of functional connections was stable over time within 30min of continuous analysis and over a 5 day period. With the same electrode montage the pattern of functional connectivity varied from one subject to another. Analysis of the temporal relationship of maxima of gamma waves between various brain areas could be a useful tool for investigation of functional connections between these brain areas. This approach could be applied for analysis of functional alterations occurring in these connections during different behavioral tasks and during processes related to learning and memory. The specificity in the connectivity pattern from one subject to another can be explained by the existence of unique functional networks for each subject.