A recently developed robotic platform termed “Genepaint” can carry out large‐scale nonradioactive in situ hybridization (ISH) on tissue sections. We report a series of experiments that validate this novel platform. Signal‐to‐noise ratio and mRNA detection limits were comparable to traditional ISH procedures, and hybridization was transcript‐specific, even in cases in which probes could have hybridized to several transcripts of a multigene family. We established an atlas of expression patterns of fibroblast growth factors (Fgfs) and their receptors (Fgfrs) for the embryonic day 14.5 mouse embryo. This atlas provides a comprehensive overview of previously known as well as novel sites of expression for this important family of signaling molecules. The Fgf/Fgfr atlas was integrated into the transcriptome database (www.genepaint.org), where individual Fgf and Fgfr expression patterns can be interactively viewed at cellular resolution and where sites of expressions can be retrieved using an anatomy‐based search. Developmental Dynamics 234:371–386, 2005. © 2005 Wiley‐Liss, Inc.