Fine needle aspiration biopsy (FNAB) is a well established method for diagnosing breast lesions, including cancers. FNAB does not require surgery and uses only a small amount of material. FNAB can also be used to acquire material for special studies. This is especially useful with small tumors (< or = 1 cm) when most of the material is needed to make a histologic diagnosis. Immunostaining techniques can be used on FNABs to investigate proliferation by bromodeoxyuridine uptake or Ki-67 labeling. Immunostaining techniques can also be used to identify oncoprotein expression, such as of p53. Fluorescence in situ hybridization is a technique that can be used to gather cytogenetic information directly from interphase tumor cells and is well suited for use with FNAB material because the harvested nuclei are intact and no cumbersome dissociation processing is needed. Flow cytometric techniques can be applied to FNAB material to study DNA content and S-phase fraction. Material acquired by FNAB can also be analyzed by the polymerase chain reaction followed by mutation detection. In this report, the authors show the applicability of these various analytic approaches to FNAB material from primary breast cancers. They show that it is essential that the FNAB harvest is representative, ample, and well prepared for the success of these studies.