Abstract: Objective To evaluate the application of retrospective spatial and temporal permutation scanning statistic and circular distribution method in the clustering detection of hand foot and mouth disease (HFMD). Methods The retrospective spatial and temporal permutation scanning statistics was used to analyze the incidence data of HFMD in Bao'an district in 2015 with SaTScan 9.4, the results were compared with the clustering information obtained from circular distribution method. Results Six possible HFMD clusters were identified from January 2015 to December 2015 in Bao'an, i.e. the cluster in Xixiang (4 May 2015-12 July 2015, P0.01), the cluster in Xin'an (2 May 2015-11 July 2015, P0.01), The cluster in Fuyong (7 May 2015-8 July 2015, P0.01), the cluster in Shiyan (9 May 2015-12 July 2015, P0.01), the cluster in Shajing (18 May 2015-9 July 2015, P0.01),and the cluster in Songgang (20 August 2015-5 October 2015, P0.01).These clustering signals were partially consistent with those from circular distribution methods and would be more sensitive in early detection of HFMD outbreak. Conclusion Retrospective spatial and temporal permutation scanning statistic is effective in evaluating the spatial and temporal clustering of HFMD and providing evidence to identify the patterns of HFMD transmission and develop effective HFMD prevention and control measures.