Introduction: Micronuclei (MN) has been used as a biomarker for assessment of DNA damage. Fine needle aspiration cytology (FNAC) is used as primary tool in diagnosis of breast lesions. Micronucleus test is simple test which is done on routine staining, avoiding the need of expensive methods. Objective: The aim of the present study was to score and compare the frequency of spontaneously occurring micronuclei in benign and malignant breast lesions. Materials and methods: A retrospective study of 50 FNAC smears of breast lesions was included in the study. The Haematoxylin and eosin stained smears were retrieved and examined for counting the micronucleus. MN was counted in 1000 epithelial cells under oil immersion. The average score was compared between benign, atypical ductal hyperplasia and malignant lesions. Results: 50 cases were included (benign cases: 27, atypical ductal hyperplasia: 4 and malignant cases: 19). The mean ± SD of micronucleus score in benign, atypical ductal hyperplasia and malignant lesions was 0.7± 0.6 (range 0–2), 4.7 ± 1.2 (range 3–6 ) and 15.2 ± 4.9 (range 8–28 ) respectively. The difference in the average micronuclei score between the three groups were statistically significant (p <0.05). Conclusion: Micronuclei score was found to be low in benign, borderline in atypical ductal hyperplasia and high in malignant lesions. It proves gradual increase of genomic damage from benign to malignant cases and serve as a tool in classification of breast lesions