Members of the Fox gene family exhibit remarkably restricted patterns of expression where they have interesting, required functions during development. We have analyzed the developmental expression patterns of three members of the Fox gene family, FoxJ1.2, FoxJ2, and FoxQ1, which have not been previously described in Xenopus. FoxJ1.2 is expressed in the otic vesicle during late neurula stages and is then also expressed in the presumptive nephrostomes of the pronephros during tailbud stages. FoxJ2 is expressed in the notochord and ventral portion of the neural tube. FoxQ1 is expressed specifically in the pharyngeal pouches as early as neurula stages and remains on in pharyngeal tissue throughout the tailbud stages. At later stages, FoxQ1 is also expressed in the anterior gut. FoxJ1.2, FoxJ2, and FoxQ1 may prove to be useful tissue-specific markers of these embryonic structures.