The Transfusion Safety Study (TSS) is a cooperative investigation of factors that determine the occurrence of and modify the expression of transfusion-transmitted infections. A major component of its data is derived from lymphocyte immunophenotyping using a large panel of monoclonal antibodies and two-color flow cytometric analysis. The multicenter longitudinal character of TSS necessitates a uniformity of instrumentation, reagents, and protocols, as well as an intensive quality control program. The baseline assessment of a cohort of males 10 years of age and over with congenital clotting disorders (CCD) exemplifies the approach and some of the flow cytometry results. A comparison of anti-HIV-1 positive and negative subjects shows that more of the loss of T4+ cells was attributable to a decrease in the T4+4B4+ subset than the T4+2H4+ subset. There was an overall increase in CD8 cells, with a significant increase in the I2+T8+ and Leu7+T8+ cells, but a fall in NKH.1+T8+ cells. Monocytes, MO2+I2+ cells, increased. In CCD patients under the age of 10, both anti-HIV-1 positive and negative, there were absolute elevations in immunocytes, including CD4. There was also a distinctly different distribution of CD4 subsets. The suppressor inducer subset, 2H4+T4+, was increased relative to the helper inducer subset, 4B4+T4+, in the younger subjects.