Breast cancer remains a major public health concern, especially in the female population, and its treatment remains challenging in the world. Targeted gene therapy might prove effective in curbing the prevalence. This Pilot study was to evaluate mutation patterns in Adenomatous Polyposis Coli (APC) And Myelocytomatosis (MYC) gene in benign and malignant breast lesions. The pilot study consisted the use of 10 formalin-fixed heterogenous paraffin-embedded tissue blocks, 5 fibroadenomas (FA) and 5 invasive ductal adenocarcinomas (IDA) from the pathological archives of Federal Teaching Hospital Ido-Ekiti. Nucleic acid amplification technique by using Dellaporta DNA extraction protocol. Polymerase chain reaction (PCR) technique was used to amplify the DNA fragments, sequenced using a Genetic Analyzer 3130xl sequencer from Applied Biosystems using the manufacturers’ manual, Bio-Edit software and Mega 6 were used for all genetic analysis. PCR optimization and Primer specificity, HGVSc, HGVSp, and VAF (%) were analysed. The results were reported that in fibroadenoma in the APC gene, single nucleotide polymorphism (SNP) mutation recorded transition in all samples, as well as in the invasive ductal adenocarcinoma it recorded. In functional mutation in the APC gene, fibroadenoma showed both silent and missense mutations while invasive ductal adenocarcinoma it recorded only missense mutation. The results reported in the MYC gene show that in SNPs mutation for fibroadenoma, showed both transversion and transition. In IDA, transition, InDel and transversion were observed. In functional mutation, fibroadenoma showed silent and missense while in IDA silent and missense were observed. This study carried out demonstrated missense mutation in both APC and MYC genes in fibroadenoma and invasive ductal adenocarcinoma singly.