Proteomic profiles of tumor protein expression by the surface enhanced laser desorption-ionization time of flight (SELDI-TOF) methodology have been shown to have a potential usefulness for protein discovery as well as screening, diagnosis, prognosis and therapeutic considerations of cancer from several organ systems. Fine-needle aspiration (FNA) specimens from tumor samples is an accepted method to diagnose the cells of interest but often can be a limited assessment due to quantity of the sample. The current use of fresh or rapidly frozen specimens for proteomic profiling can be burdensome for clinicians to collect and submit specimens. The current study tests the hypothesis that placement of FNA and other cytological material in PreservCyt may be an acceptable method of sample handling for protein profiling evaluation by this method though it may not be suitable for true protein discovery or characterization. Excised fresh breast tissue for evaluation and/or treatment of a variety of breast lesions were sampled by FNA technique and placed into PreservCyt. These samples were then homogenized under denaturing conditions and evaluated by the SELDI-TOF methodology. Most samples collected showed a satisfactory quantity of protein for analysis by the SELDI-TOF methodology. Protein patterns from a variety of benign and malignant lesions revealed reproducible patterns on triplicate testing. Benign lesions had similar protein patterns across age groups in this limited series that may have potential diagnostic significance. In conclusion, FNA of breast tissue placed in PreservCyt is a potentially acceptable method of sample handling for evaluation by the SELDI-TOF methodology for establishment of reproducible protein patterns. Preliminary results from a spectrum of breast lesions suggest these patterns may have potential for ancillary testing for diagnostic consideration of breast lesions. This collection methodology could simplify sample gathering for further testing of all types of cytological specimens by the SELDI-TOF methodology. Larger studies will be needed to assess this methodology as a diagnostic aid.