We developed a decision-support system, the flow cytometry workstation (FCW), that provides variable panel definitions, age-adjusted reference ranges, and graphic display of immunologic trends. Automated quality assurance functions include validation of flow cytometry data using user-defined monoclonal antibody sums and delta check computations. We evaluated the FCW to determine whether it would reduce CD4+ technical and clerical errors and to discover patterns or trends within flow cytometric data for research purposes. The FCW reduced the number of technical and clerical errors in its first 2 years of use (P = .003). User-defined quality assurance summation checks such as CD2+ + CD20+ = 95% +/- 5% were applied to a 10-year data set as part of a retrospective analysis. The FCW discovered a relationship between specimen processing and the number of results appearing out of range: 58.11% of reported samples appeared out of range in 1993 compared with 2% in 1996 (P1 < .001). The FCW is a foundation for quality improvement and outcomes-based research for clinical flow cytometry and serves as a platform for state-of-the-art laboratory management.