We developed a flow cytometry‐based assay, termed Differential Leukocyte Counting and Immunophenotyping in Cryopreserved Ex vivo whole blood (DLC‐ICE), that allows quantification of absolute counts and frequencies of leukocyte subsets and measures expression of activation, phenotypic and functional markers.We evaluated the performance of the DLC‐ICE assay by determining inter‐operator variability for processing fresh whole blood (WB) from healthy donors collected at multiple clinical sites. In addition, we assessed inter‐operator variability for staining of fixed cells and robustness across different anticoagulants. Accuracy was evaluated by comparing DLC‐ICE measurements to real‐time cell enumeration using an accredited hematology analyzer. Finally, we developed and tested the performance of a 27‐colour immunophenotyping panel on cryopreserved fixed WB and compared results to matched fresh WB.Overall, we observed <20% variability in absolute counts and frequencies of granulocytes, monocytes and lymphocytes (T, B and NK cells) when fresh WB was collected in different anti‐coagulant tubes, processed or stained by independent operators. Absolute cell counts measured across operators and anti‐coagulants using the DLC‐ICE method exhibited excellent correlation with the reference method i.e complete blood count (CBC) with differential, measured using a hematology analyzer (r2>0.9 for majority of measurements). A comparison of leukocyte immunophenotyping on fresh WB vs DLC‐ICE processed blood yielded equivalent and linear results over a wide dynamic range (r2=0.94 over 10‐104 cells/μL).These results demonstrate low variability across trained operators, high robustness, linearity and accuracy, supporting utility of the DLC‐ICE assay for large cohort studies involving multiple clinical research sites.This article is protected by copyright. All rights reserved.