It is now universally accepted that DNA is the main target for damages caused by physical and chemical genotoxicants. Although there are different methods to measure directly the induced DNA damages but due to fast repair processes in cellular environment, most of the damages would be repaired even before sampling, therefore processed DNA damages, i.e. damages left unrepaired after acting repair machinery is preferable to measure in various exposure scenarios. Various cytogenetic end points are introduced and implemented such as metaphase analysis, sister chromatid exchanges, premature chromosome condensation, translocation assay and micronucleus assay. All of these methods were extensively used for various purposes but among them micronucleus (MN) assay was found more practical because of ease of scoring, potential for automation as well as being nearly as sensitive as other procedures. These characteristics made MN assay very popular for screening of the effects of various genotoxic agents in vitro and in vivo. In this review we try to summarize the main aspects of application of this method in radiobiological studies and genome instability related diseases.