Resting-state functional magnetic resonance imaging (fMRI) is a technique that measures the intrinsic function of brain and has some advantages over task-induced fMRI. Regional homogeneity (ReHo) assesses the similarity of the time series of a given voxel with its nearest neighbors on a voxel-by-voxel basis, which reflects the temporal homogeneity of the regional BOLD signal. In the present study, we used the resting state fMRI data to investigate the ReHo changes of the whole brain in the prelingually deafened patients relative to normal controls. 18 deaf patients and 22 healthy subjects were scanned. Kendall's coefficient of concordance (KCC) was calculated to measure the degree of regional coherence of fMRI time courses. We found that regional coherence significantly decreased in the left frontal lobe, bilateral temporal lobes and right thalamus, and increased in the postcentral gyrus, cingulate gyrus, left temporal lobe, left thalamus and cerebellum in deaf patients compared with controls. These results show that the prelingually deafened patients have higher degree of regional coherence in the paleocortex, and lower degree in neocortex. Since neocortex plays an important role in the development of auditory, these evidences may suggest that the deaf persons reorganize the paleocortex to offset the loss of auditory.