Antibiotic resistance genes (ARGs) have been identified as emerging contaminants in water and wastewater. Concerns have been raised of whether disinfection processes can effectively eliminate ARGs and thus mitigate their spread. Due to the different existing forms and dissemination pathways, intracellular ARGs (iARGs) and extracellular ARGs (eARGs) have different responses to disinfection processes. This review compares the elimination of iARGs and eARGs in representative disinfection processes applied at water and wastewater treatment plants, including treatment by chlorine, chloramine, chlorine dioxide, ozone, ultraviolet irradiation (UV), and combination of UV with chemicals. Meanwhile, the redistribution of ARGs upon disinfection processes is highlighted. Elimination efficiencies of ARGs generally follow the order: ozone > chlorine ≫ chlorine dioxide > chloramine. The elimination of naked eARGs could be up to 4-log higher than that of iARGs. Notably, these disinfectants and the resulting disinfection byproducts formed in disinfection process can select antibiotic resistant bacteria (ARB) and increase relative abundances of iARGs. Under practical disinfectant exposure, elevated abundances of eARGs may be observed. Low doses of chlorine and chloramine tend to enhance the transfer of ARGs from intracellular to extracellular forms. To selectively control ARGs and associated risks and meanwhile minimize the unintended consequences, the disinfection practice may warrant optimization.