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The applied bioanalytical assays used for the evaluation of human immune responses from samples collected during clinical trials must be well characterized, fully validated and properly documented to provide reliable results. Even though recommendations for the standardization of flow cytometry instrumentation and assay validation for its clinical application have been published by several organizations, definitive guidelines are not available yet. The aim of the present paper is to provide a validation approach for flow cytometry, examining parameters such as linearity, relative accuracy, repeatability, intermediate precision, range and detection limits and specificity, in order to demonstrate and document its applicability for clinical research purposes and its possible use as one of the methods for the evaluation of vaccine immunogenicity.