In the past decade, the pan-genome concept has been largely employed to investigate the bacterial comparative genomics and evolution analyses. Many programs have been developed for this purpose but a need is still present for the exploration and visualization of data derived from pan-genome analyses. To address this question, we developed a web-based application, PanExplorer, which will perform pan-genome analysis based on the PGAP pipeline and expose resulting information as a comprehensive and easy way, through several modules facilitating the exploration gene clusters and interpretation of data. The application allows interactive data exploration at different levels : - Pan-genome visualization as a presence/absence heatmap. This overview allows to easily identify and distinguish core-genes (present in all strains), cloud genes (genes from the accessory genome) and genome-specific genes. - Physical map of core-genes and strain-specific genes can be displayed as a circular genomic representation (Circos), for each genome taken independently. - Synteny analysis. The conservation of gene order between genomes can be investigated using graphical representations - Visual inspection of a specific cluster. Thanks to the use of NCBI Entrez API, the application guarantees an up-to-date availability of public genomes, to be analyzed on-the-fly, and represents a versatile tool for genome exploration filling a need for bacteriologist community. Among perspectives and further development, new functionalities might be implemented shortly such as on-line pan-genome wide association studies (pan-GWAS) based on Scoary software or COG enrichment statistical studies. PanExplorer is written in Perl CGI and relies on several Javascript libraries for visualization. It is freely available at http://panexplorer.southgreen.fr.