OBJECTIVE: Stereotaxic core biopsy provides intact samples of breast tissue for accurate histologic analysis. We conducted a study to determine if prognostic data could also be successfully derived from such core samples and how the data correlate with surgical biopsy. MATERIALS AND METHODS. Both core and surgical breast biopsies from 135 patients were processed under a uniform flow cytometry protocol. Samples were coded and then randomly processed at an outside flow cytometer and interpreted by an independent pathologist; the code was broken and patients' results correlated only after all samples were completely analyzed. RESULTS. Core breast biopsy provides intact tissue that can be successfully processed by a flow cytometer, even after being embedded in paraffin for initial histologic analysis. Larger cores (14 gauge) had fewer insufficient samples, as recorded on ploidy histograms. Although ploidy may reflect the underlying aggressiveness of a lesion and assist in evaluating breast cancer, surgical-pathologic correlation with stereotaxic biopsy indicated, as has been confirmed in other studies, considerable overlap of different ploidy types between benign and malignant conditions. There was no correlation between mammographic presentation and ploidy or S- phase fractions. CONCLUSION. Stereotaxic large-core biopsy can enable accurate histologic diagnosis of breast disease and furnish sufficient tissue for flow cytometric measurements of ploidy and S-phase fractions, even at an interval following paraffinization. Such prognostic information aids in planning of adjuvant therapy, allows flexibility should surgery fail to provide enough tissue for DNA study, and helps radiologists further market stereotaxic biopsy to clinicians.