Zebrafish embryos are well suited as a model system to perform chemical biology experiments effectively in educational settings. We studied the effect of caffeine on heart rate (HR) and other phenotypes of zebrafish embryos using visual microscopy and simple imaging. Acute treatment with millimolar concentrations of caffeine in embryo medium caused a dose-dependent decrease in HR in 2-3-day-old zebrafish embryos, ultimately resulting in complete HR cessation. A characteristic pattern of decrease in HR was observed, with an initial acute drop in HR and a period of stabilization followed by complete cessation. The effects of caffeine were not reversed by cotreatment with ruthenium red and adenosine, agents known to be antagonistic to caffeine, or by changes in calcium concentration in embryo medium. Apparent cardiac arrhythmia and a typical kinking effect in the trunk/tail region were also observed because of caffeine treatment. Our results, taken together with previous reports, raise the possibility that caffeine exerts its effects on embryonic HR of zebrafish by inhibition of ether-a-go-go potassium channels. However, further experimentation is required to dissect the molecular basis of caffeine action. We demonstrate that such experiments can be used to explore the effect of small molecules, such as caffeine, on cardiovascular phenotypes and to encourage experimental design in chemical biology. © 2010, Mary Ann Liebert, Inc.