The primary immunodeficiency diseases (PIDs) encompass an extremely large and diverse number of clinical disorders caused by mutations in genes that affect virtually every measurable component of our immune systems. Many of the genetic mutations lead to abnormalities that can be detected in circulating peripheral blood cells of suspected patients by flow cytometry and the appropriate combinations of reagents and in vitro manipulations. The flow cytometry procedures that have been developed to detect abnormalities in peripheral blood cells of primary immunodeficiency patients can barely be covered in an entire book, let alone one chapter. Instead of attempting to cover each disease with a specific assay or test, we review three procedures each covering a global aspect of the observed immune abnormality, i.e., detection of lymphocyte subset abnormalities, lymphocyte "marker" abnormalities, and leukocyte function abnormalities.