Background: A micronucleus (MN) is a small additional nucleus, morphologically identical to but smaller than the main nucleus. It is a sensitive indicator of chromosomal instability, and it can be detected in fine-needle aspiration (FNA) smears with the Giemsa stain by light microscopy and the acridine orange (AO) stain by fluorescent microscopy. The objective of this study was to analyze the MN score in FNA smears of patients with breast carcinoma and fibroadenoma (FA). Materials and Methods: This was a prospective observational study which included 78 cases of infiltrating duct carcinoma (IDC) and 82 of FA (as controls). Giemsa- and AO-stained FNA smears were analyzed and MN scores were compared between the IDC and FA cases. Results: The mean MN scores of the FA and IDC groups were 0.28 ± 0.45 and 11.28 ± 7.22 in the AO-stained smears and 0.13 ± 0.34 and 9.79 ± 6.5 in the Giemsa-stained smears (P = 0.0002 and 0.0001), respectively. The MN score increased in a stepwise manner from FA to Grade I, II, and III of IDC in Giemsa-stained smears. Comparisons of mean MN score between FA and the three different grades of IDC and between Grade I and II and Grade III were statistically significant (<0.001 in each category). Although the mean MN score with AO stain was higher than the mean MN score with Giemsa stain, this difference was not statistically significant (P = 0.17). Conclusion: The MN score in FNA smears in the IDC group was significantly higher than in the FA group, suggesting that it can be used as a potential additional surrogate marker for diagnosing and grading breast carcinoma. Both AO and Giemsa stains were equally good for MN scoring of the FNA smears.