Background: ATM is a Phosphatidylinositol-3-Kinase–Related Kinase(PIKKs), belonging to a family of serine/threonine kinases that also contains DNA-Dependent Protein Kinase (DNA-PK), which plays a role in the DNA Double-Strand Break (DSB) repair pathway of Non-Homologous End Joining (NHEJ), and Mammalian Target of Rapamycin (mTOR), a key autophagy regulator. ATM recognizes and amplifies the signal generated by double strand break, upon activation, CHK2 are released from chromatin and halt cell cycle progression to allow repair. The aim was to study the mutation of Ataxia telangiectasia gene and Chek2 gene in a malignant and benign breast lesion. There is a hitch in the comprehension of the concept of carcinogenesis thus, changes that occur to genes which cause cells to malfunction, causing them to grow and divide when they should not is not well understood. Materials and Methods: A total of ten formalin fixed, paraff in embedded tissue blocks, consisting of five fibroadenoma of the breast and five invasive ductal carcinoma, were retrieved from the Pathological Archives of Federal Teaching Hospital Ido-Ekiti. The tissue blocks were analysed with the use of Nucleic acid amplification techniques and the results were presented in SNPs and functional mutation through graphs and charts. Results: The results of the study showed that in ATM gene; Fibroadenoma SNPs observed, 63.7% insertion, 27.3% Transversion and 9.1% Transition. Functional mutation in fibroadenoma observed 100% Missense, 0% Nonsense and Silent. In invasive ductal carcinoma SNPs observed, 55.5% Transversion, 33.3% Insertion and 11.1% Transition. Funcional mutation in invasive ductal carcinoma observed, 49.95% Missense and Silent and 0% Nonsense. Comparison between fibroadenoma samples is 0. The comparison between invasive ductal carcinoma samples is 0. The comparison between fibroadenoma and invasive ductal carcinoma samples is 0.0048. In Chek2 gene; Fibroadenoma SNPs observed, 45% Transition, 44% Transversion and 11% Indel. Functional mutation in fibroadenoma observed 78% Missense, 22% Silent and 0% Nonsense. In invasive ductal carcinoma SNPs observed, 55% Transition, 33% Transversion and 12% Indel. Funcional mutation in invasive ductal carcinoma observed, 67% Missense, 33% Silent and 0% Nonsense. Comparison between fibroadenoma samples is 0. The comparison between invasive ductal carcinoma samples is 0. The comparison between fibroadenoma and invasive ductal carcinoma samples is 0.0333.Conclusion: Impairment of DNA damage response during the process of malignant transformation may promote and/or fuel tumorigenesis leading to accumulated genetic lesions and increased genomic instability therefore, mutations of ATM and CHK2 genes are frequently found in tumors and predispose to cancer development.