Flow cytometers are instruments that can determine multiparameter data simultaneously and have a great potential in providing unique information about cells. The FACSCount System is designed as the first dedicated flow cytometer for the clinical laboratory. Its current configuration provides CD4, CD8, and CD3 absolute counts from 100 microliters of whole blood. Adapting the FACSCount System to the clinical setting are minimal sample handling, lysis free cell preparation, automated fluorescence gating, built-in calibrated reference beads, and appropriate error code reporting. Quality control checks ensure that reported CD4 counts, important for clinical follow-up and patient management, are accurate, precise, and reproducible across instruments over time.