Glucocorticoids (GCs) constitute one of the most powerful classes of anti-inflammatory agents and are used for the treatment of a plethora of diseases related to autoimmunity, allergy, cancer, and infection. In the last two decades, multiple studies using genetically engineered mice with targeted deletions of the GC receptor (GR) in individual cell types have provided insights into the mechanisms of GCs in the control of the immune system. The characterization of GR expression in these mouse models, however, mostly relied on the analysis of mRNA expression or reporter gene activity. In contrast, approaches directly detecting the GR protein on a cellular level are scarce. Thus, we here used a flow cytometric method to analyze mice in which the GR gene locus was disrupted with the help of a Cre recombinase expressed under the control of either the lck or the lysM promoter. Measuring GR protein expression in immune cell subpopulations unveiled an efficient and highly selective depletion in both strains of knock-out mice in accordance with the expected cellular specificity of the employed promoters for T cells or myeloid cells, respectively. The flow cytometric data were well in line with those from the analysis of GR mRNA expression in magnetically sorted immune cell subpopulations but they could be obtained much more quickly. In summary, our data indicate that flow cytometry is a powerful tool with which to define GR protein content at a single cell level when studying the function of GCs in the immune system.