In situ hybridization involves the hybridization of an antisense RNA probe to an mRNA transcript and it is a powerful method for the characterization of gene expression in tissues, organs, or whole organisms. Performed as a whole mount (WISH), it allows the detection of mRNA transcripts in three dimensions, while combined with sectioning, either before or after hybridization, it provides gene expression information with cellular resolution. FISH relies on the fluorescence detection of probes and is the method of choice for the simultaneous detection of transcripts with similar or overlapping expression patterns, as each can be clearly distinguished by the selection of fluorophore. Here, we describe a protocol for performing multicolor FISH in Xenopus embryos in whole mounts and sections that can be further combined with antibody staining.