Flow cytometric analysis of leukocyte surface antigens has been used to characterize infectious and septic processes in patients. We wanted to investigate how the sampling and processing temperature, the anticoagulant used, and the storage of the sample influence leukocyte immunophenotyping. Four blood samples, two using acid citrate dextrose and two using heparin as an anticoagulant, were taken from five intensive-care unit patients with severe sepsis and five healthy volunteers. The samples were collected, stored, and processed either at +4°C or at room temperature (RT). The samples were processed for flow cytometric analysis within 1 hr of collection or after 6 or 24 hr storage. The surface antigens of interest were neutrophilic CD11b and CD64, monocytic CD11b, CD14, CD40, CD64, CD80 and HLA-DR, and lymphocytic CD69 (separately in CD4+ and CD8+ T cells, B cells, and natural killer cells). The fluorescence intensities were higher at RT than at +4°C. During storage the intensities increased at RT, but at +4°C there were only minor changes. The effects were similar with both anticoagulants studied. According to our results, flow cytometric analysis of leukocyte surface antigen expressions should be performed using +4°C temperature throughout the process and within 6 hr. J. Clin. Lab. Anal. 25:118–125, 2011. © 2011 Wiley-Liss, Inc.