Reef coral fluorescent proteins (RCFPs) are bright fluorescent proteins (FPs) covering a wide spectral range. We used various RCFP genes to transgenically color different cell populations in the brain. The mouse Thy1.2 promoter was used to target expression of HcRed1 in neurons, the human glial fibrillary acidic protein (GFAP) promoter to label astrocytes with AmCyan1, AsRed2 and mRFP1 as well as the mouse proteolipid protein promoter to mark oligodendrocytes with DsRed1. In brain sections of transgenic mice, RCFP expression was found to be highly specific using immunohistochemistry and fluorescence microscopy. In contrast to transgenic mice with expression of jellyfish FP variants, RCFPs formed numerous fluorescent precipitates. These aggregates were primarily found in cell somata and also in cell processes. Older mice were more affected than younger ones. Despite these fluorescent deposits, physiological properties of RCFP expressing brain cells such as whole-cell membrane currents or glutamate-evoked calcium signaling seemed to be unaffected. While brightness and spectral variation of RCFPs are optimal for expression in transgenic animals used in physiological experiments, the formation of fluorescent precipitates in various cell types limits their use for morphological cell analysis in situ.