Flow cytometry techniques for immunophenotyping have revolutionised the diagnosis and monitoring of paediatric immunological disorders. Although recent studies in adult subjects discourage the use of density gradients for cell preparation prior to phenotyping, these procedures continue to be used. The purpose of this study was to determine the effect of density gradient separation on lymphocyte phenotypes from neonates, infants, and adults as compared to whole blood determinations. Subset distributions were different with the two procedures. In all three groups, CD19+ (B cell) and CD8+ (suppressor/cytotoxic T cell) percentages were significantly lower and CD3-CD56+ (NK cell) percentages were significantly higher in the density gradient separated cells. The loss of CD8+ cells in density gradient separation was shown to be a selective event. The CD8+CD11b- (cytotoxic T) subset percentages were lower in the density gradient separated cells, while the percentages of CD8+CD11b+ (suppressor T) cells were not affected by separation procedure. Because of the selective loss of lymphocytes on density gradients, the use of a whole blood technique for immunophenotyping in paediatric subjects is recommended.