This publication outlines an approach for the validation of flow cytometry methods used in the analysis of a wide range of biomarkers. It is written as a guidance document for method validation in a GLP environment, and from the viewpoint of the pharmaceutical industry, but its relevance is wide-ranging. The approach to method validation described is intended as a starting point for further discussion, as well as providing reference material to colleagues developing fit-for-purpose flow cytometry methods. Pre-validation steps are discussed as prerequisite assessments to determine method and reagent suitability, and to minimise variables during the full validation process. The guide to method validation takes account of the many flow cytometry assay types in use, and provides guidance on the types of assessments necessary to produce a fit-for-purpose method suitable for use in a regulatory environment.