We have previously shown that analyses of autocorrelation of BOLD signal applied to single voxels in healthy controls can identify gradients of temporal dynamics throughout the hippocampal long-axis that are related to behavior. A question that remains is how changes in functional and structural integrity in the brain affect single voxel autocorrelation. In this study we investigate how hippocampal autocorrelation is affected by structural and functional hippocampal dysfunction by investigating a population of patients with unilateral temporal lobe epilepsy (TLE). Many patients with TLE have mesial temporal sclerosis (MTS), characterized by scarring and neuronal loss particularly in the anterior hippocampus. Here we compared patients with left and right TLE, some with and without MTS, to healthy controls. We applied our single voxel autocorrelation method and data-driven clustering approach to segment the hippocampus based on the autocorrelation. We found that patients with left TLE had slower signal dynamics (i.e., higher autocorrelation) compared to controls, particularly in the anterior-medial portion of the hippocampus. This was true for both the epileptogenic and non-epileptogenic hemispheres. We also evaluated the extent of cluster preservation (i.e., spatial overlap with controls) of patient autocorrelation clusters and the relationship to verbal and visuospatial memory. We found that patients with greater cluster preservation in the anterior-medial hippocampus had better memory performance. Surprisingly, we did not find any effect of MTS on single voxel autocorrelation, despite the structural changes associated with the condition. These results suggest that single voxel autocorrelation may be related to functional, rather than structural, integrity.