The aim of this study is to analyze the effect on histopathological changes and Ki-67 expression levels of Flattening Filter (FF) and Flattening Filter Free (FFF) beams to investigate the radiobiological mechanisms underlying laryngeal cancer (LCa) post-radiotherapy (RT) on mice models.Forty adult NOD SCID gamma (NSG) mice models were randomly divided into four groups; the sham, LCa, FF-RT and FFF-RT groups. The head and neck region of mice in FF-RT and FFF-RT groups (LCa plus RT groups) were irradiated with a single dose of 18 Gy at 400 MU/min and 1400 MU/min. The NSG mice received radiotherapy 30 days after tumor transplantation and sacrificed 2 days after radiotherapy for analysis of histopathology parameters and K-67 expression levels.Comparing the LCa, FF-RT and FFF-RT groups with the sham group, statistically significant differences were observed in histopathological parameters depending on tumor tissue and dose rate (p < 0.05). When the histopathological effects of FF-RT beam on LCa tissue were compared with FFF-RT beam, it was observed that statistically significant differences occurred (p < 0.05). Comparing the LCa group with the sham group, it was observed that the Ki-67 level affected significantly depending on the development of cancer (p < 0.01).It was concluded that FF and FFF beams caused significant changes in the histopathological parameters and Ki-67 expression levels. When the effects of FFF beam on Ki-67 levels, cell nucleus and cytoplasmic findings were compared with FF beam, significant radiobiological differences were observed.