Flavonoids are named after the word 'flavus', which means 'yellow' in Latin. These are pigment compounds found in many plants as a member of polyphenolic molecules that share different chemical structures and properties. These molecules with therapeutic properties are among the basic components of the human diet. In our study, the effects of some flavonoids such as hesperidin, quercetin and naringenin on the activity of the enzyme Acetylcholine Esterase (AChE) in the brain and eye tissues of rats were evaluated. Animal experiments and procedures were carried out in accordance with national rules for the use and care of laboratory animals and were approved by Atatürk University Experimental Animals Ethics Committee (22.02.2018, 75296309-050.01.04). For this purpose; a healthy group and seven experimental (n = 6) groups (control group, radiotherapy group, hesperidin group, quercetin group, naringenin group, hesperidin + radiotherapy group, quercetin + radiotherapy group and naringenin + radiotherapy) were created. AChE enzyme activity was determined for each tissue and organ sample obtained. All experimental results were calculated as mean EU / mL ± Standard Deviation (± SD). When the obtained results were examined, there were significant differences between the control group and seven experimental groups in terms of AChE enzyme levels of brain and eye tissues. In fact, when compared with the control group and the seven experimental groups, significant reductions in AChE levels were observed in the brain and eye tissue, and these flavonoids showed a protective effect against damage caused by radio therapy by inhibition of the AChE enzyme.