We describe here a fast procedure to identify, by Pulsed Field Gel Electrophoresis (PFGE), circular DNA molecules, displaying shift mobility dependent on ethidium bromide (EtBr) concentration. Several identical DNA samples were coelectrophoresed in a multilane gel with different EtBr concentrations in each lane. Samples were run in a Contour Clamped Homogeneous Electric Field (CHEF) or in a small CHEF (miniCHEF) equipment for 15 or 4 h, respectively. Circular DNA molecules from the protozoan parasiteEntamoeba histolyticawere detected in a single running. The circles were isolated from the gels and then their structure was confirmed by transmission electron microscopy. By hybridization it was shown that the circles obtained corresponded to the ribosomal DNA episome.