To test the idea that caffeine might induce changes in gene expression in the honeybee brain, we contrasted the transcriptional profiles of control and caffeine-treated brains using high-throughput cDNAmicroarrays. Additional quantitative real-time PCR was performed on a subset of eight transcripts to visualize the temporal changes induced by caffeine. Genes that were significantly upregulated in caffeine-treated brains included those involved in synaptic signaling (GABA:Na symporter, dopamine D2R-like receptor, and synapsin), cytoskeletal modifications (kinesin and microtubule motors), protein translation (ribosomal protein RpL4, elongation factors), and calcium-dependent processes (calcium transporter, calmodulin-dependent cyclic nucleotide phosphodiesterase). In addition, our study uncovered a number of novel, caffeine-inducible genes that appear to be unique to the honeybee. Time-dependent profiling of caffeine-sensitive gene expression shows significant upregulation 1 h after treatment followed by moderate downregulation after 4 h with no additional changes occuring after 24 h. Our results provide initial evidence that the dopaminergic system and calcium exchange are the main targets of caffeine in the honeybee brain and suggest that molecular responses to caffeine in an invertebrate brain are similar to those in vertebrate organisms.