I am planning to perform intracellular cytokine staining by flow cytometry on cells derived by MACS Cell Separation. Will the magnetic beads interfere with intracellular staining?

MACS MicroBeads will not interfere with intracellular cytokine staining and flow cytometric analysis. The beads do not influence the scatter or fluorescence profiles of the cells. It is even possible to perform a fluorescence staining before fixing the cells with the same antibody (e.g., CD4 or CD8) that was used for separation. 

Learn more about MACS MicroBeads in the MACS Handbook.