Cell-type-specific analysis of gene expression and chromatin profiling requires the isolation of discrete cell populations from complex pools. However, until now this most critical step has been labor intensive and technical challenging. Here, we describe a rapid protocol based on fluorescence-activated cell sorting (FACS) for cell-type-specific RNA and chromatin profiling. We detail how to isolate nuclei from Arabidopsis inflorescence and silique homogenates and how to purify endosperm nuclei labeled by nuclear-targeted green fluorescent protein using FACS. The purified fluorescent endosperm nuclei can be further used for chromatin immunoprecipitation (ChIP) followed by hybridization to high-resolution whole-genome tiling microarrays (ChIP-on-chip) or transcriptional profiling.