Voxel-based morphometry (VBM) studies have provided cumulative evidence of gray matter (GM) atrophy in patients with Parkinson's disease with dementia (PDD) relative to healthy controls (HC). However, not all the studies reported entirely consistent findings. A systematic search for VBM studies of PDD patients and HC subjects published in PubMed and Embase databases from January 2000 to June 2012 was conducted. Meta-analysis was performed by using a newly improved voxel-based meta-analytic technique, effect size signed differential mapping, to quantitatively explore the GM abnormalities between PDD patients and HC subjects. A total of 6 cross-sectional VBM studies involving 105 PDD patients and 131 HC subjects met the inclusion criteria. Considerable regional GM decrease was detected in the medial temporal lobe (MTL) and basal ganglia. The findings of the present study remained largely unchanged in the entire brain jackknife sensitivity analyses. Meta-regression showed dementia severity correlated with the left MTL. The present meta-analysis provided evidence of PDD-related GM atrophy, which suggested MTL and basal ganglia were implicated in PDD. This finding could give us further insight about the pathophysiological basis revealed by structure abnormalities in PDD.