Abnormalities in the number and percent of CD3, CD4, and CD8 T cells have been described in a number of different disease conditions. In patients who are infected with HIV, the CD4 count is measured for AIDS diagnosis and for initiation of antiviral therapy. The progressive loss of CD4 T lymphocytes in patients infected with HIV is associated with increased infections and complications. The Public Health Service has recommended that all HIV-positive patients be tested every 3 to 6 months for the level of CD4 T lymphocytes.

Basic T-cell subset quantitation is also very useful in the evaluation of patients with primary cellular immunodeficiencies of all ages, including follow-up for newborn screening for severe combined immunodeficiency and immune monitoring following immunosuppressive therapy for transplantation, autoimmunity, or any other relevant clinical condition where immunomodulatory treatment is used, and the T-cell compartment is specifically affected.

It is also helpful as a preliminary screening assay for gross quantitative anomalies in T cells, whether related to malignancies or infection.