Staining of transcription factors (TFs) together with retention of fluorescent reporter proteins is hindered by loss of fluorescence using current available methods. In this study, it is shown that current TF staining protocols do not destroy fluorescent proteins (FPs) but rather that fixation is not sufficient to retain FPs in the cytosol of the permeabilized cells. In this article, a simple and reliable protocol is elaborated, which allows efficient TF and cytokine staining while retaining FPs inside fixed cells. V C 2014International Society for Advancement of Cytometry Key terms EYFP; RFP; EGFP; FoxP3; RORct; T-bet; flow cytometry; fixation; fate mapping; formaldehyde; mouse T cells TO address the functions of cells and genes and their expression patterns, reporter mice are used. These mice often express cytosolic-soluble fluorescent proteins (FPs) under direct control of a tissue-or cell-type-specific promoter. Alternatively, and often for fate mapping projects, mice with conditional expression of FPs from the Rosa26 locus are used (1). Because of a loxP-flanked transcriptional STOP cassette preceding the FP gene, the latter is only expressed in cells in which a specific Cre-recombinase is or was active. Fate mapping mice constitute a very useful tool to study cell differentiation and to trace cell destiny/progeny, because of the irreversible tagging once the respective Cre was produced (2). As there is significant interest in staining lineage decision transcription factors (TFs) in fate mapping experiments, we thought to develop a method which would allow simultaneous staining of nuclear TFs such as FoxP3, RORct, or T-bet in cells which express a fluorescent reporter protein. In contrast to the common understanding, we found that the usual methods of TF detection by flow cytometry do not destroy fluorescence of the reporter proteins but rather rely on the use of too weak fixation conditions. This insufficient fixation does not retain FPs inside the cells when they are permeabilized during the TF-staining procedure. This is corroborated by the fact that reporter proteins, which are bound to the cell membrane as part of fusion proteins, for example, in case of the DTR-GFP in DEREG mice (3), do not lose their fluorescence on FoxP3 staining using standard FoxP3 staining protocols (3). The inherent problem seems that stronger fixation, commonly used for cytokine staining, which is necessary to keep cytosolic proteins confined within cells during permeabilization, hinders or masks efficient staining of TFs. By varying the fixative with different timings and concentrations, we were able to define an intermediate fixation strength, which