Supraventricular tachycardias are the most prevalent group of arrhythmias observed in the fetus and infant and their incidence increases through early childhood. The molecular pathogenesis of embryonic cardiac dysfunction is poorly understood, due in part to the absence of imaging techniques that provide functional information at the cellular and molecular levels in the developing mammalian heart, particularly during early heart formation. The combination of protein engineering, genetic specification, and high-resolution optical imaging enables new insights into cardiac function and dysfunction during cardiac development. Here we describe the use of GCaMP2, a genetically encoded Ca(2+) indicator (GECI), to determine the processes of cardiac electrical activation during cardiac organogenesis. Transgenic specification of GCaMP2 in mice allows sufficient expression for Ca(2+) imaging as early as embryonic day (e.d.) 9.5, just after the heart begins to function at e.d. 8.5. Crosses with knockout lines in which lethality occurs due to cardiac dysfunction will enable precise determination of the conduction or excitation-contraction coupling phenotypes and thereby improve the understanding of the genetic basis of heart development and the consequence of gene mutations. Moreover, lineage-specific targeting of these sensors of cell signaling provides a new window on the molecular specification of the heart conduction system. We describe mouse lines and imaging methods used to examine conduction in the pre-septated heart (e.d. 10.5), which occurs through dramatically slowed atrioventricular (AV) canal conduction, producing a delay between atrial and ventricular activation prior to the development of the AV node. Genetic constructs including single and bi-allelic minimal promoter systems, and single allele BAC transgenes, enable general or lineage-specific targeting of GCaMP2. High-resolution imaging of embryonic heart conduction provides a new window on one of the most complex events in the mammalian body plan.