This article describes a procedure for the dissociation of zebrafish (Danio rerio) embryos to produce a suspension of single cells that is suitable for fluorescence-activated cell sorting (FACS). The method has been applied to embryos at stages from 14 h post fertilization (hpf) to larvae at 5 d post fertilization (dpf), and it has also been successfully used for isolating fluorescently tagged neurons from whole dissociated embryos and early larvae. The cell collection procedures described in this protocol may also be adapted for older embryos and juvenile zebrafish. RNA can be extracted from the sorted cells and used for subsequent quantitative real-time PCR (qRT-PCR), microarrays, or next-generation sequencing (NGS) experiments.