A variety of tumor-genetic alterations have been identified circulating free-form in the plasma and serum of cancer patients that may have diagnostic and prognostic implications. Currently, no consensus exists as to whether plasma or serum is preferable for circulating nucleic acid analysis, and the impact of collection and processing on yield is unknown. We prospectively assessed DNA content in paired plasma and serum obtained from 10 patients with AJCC stage IV advanced metastatic melanoma. Blood (30 mL) was collected from each patient as follows: 10 mL each was processed immediately for serum and plasma and an additional 10 mL was incubated overnight at 37 degrees C and processed for serum. In addition, blood was collected from 25 normal healthy donor volunteers to determine the concentration of free DNA circulating in paired plasma and serum. DNA was isolated from 800 microl of plasma or serum and quantified. Median-free DNA concentrations were fourfold greater in serum than in the corresponding plasma sample. Serum isolated from blood allowed to clot overnight yielded four times more DNA than serum processed immediately. Among normal healthy volunteers, only serum contained detectable free DNA. These findings provide conclusive evidence that elevated levels of circulating DNA could be identified consistently in patients with cancer than in normal healthy donors. Furthermore, the method of blood processing may significantly affect the levels of circulating nucleic acids and impact the investigator's results. Significant consideration must be given to the methods by which circulating nucleic acids are obtained for clinical analysis.