The aim of that in-vitro study was to evaluate and compare different irrigating solutions namely; MCJ, 2% CHX and 17%EDTA regarding: Their cytotoxic behaviour using the MTT tetrazolium assay and the surface changes at different areas of the root canal by SEM. The following conclusions were drawn: MCJ exerted a less cytotoxic effect compared with 17% EDTA and 2% CHX. The protocol of using MCJ/ EDTA showed its efficiency in complete removal of the smear layer from different areas of the root canal system.