Thin spongy myocardium is critical at early embryonic stage [before embryonic day (E) 13.5 in mice] to allow diffusion of oxygen and nutrients to the developing cardiomyocytes. However, establishment of compact myocardium at later stage ( approximately E16.5) during development is necessary to prepare for the increase in demand for blood circulation. Elucidating molecular targets of the spongy-compact myocardium transition between E13.5 and E16.5 in heart development is thus important. Previous studies demonstrated that multiple transcription factors and signaling pathways are involved in the regulation and function of the myocardium in heart development. Disruption of certain transcription factors or critical components of signaling pathways frequently causes structural malformation in heart and persistence of "thin spongy myocardium". We have recently demonstrated activation of the calcineurin/NFAT signaling pathway at E14.5 in developing myocardium. Constitutive inhibition of the calcineurin/NFAT signaling pathway caused embryonic lethality. Molecular targets downstream of the calcineurin/NFAT signaling pathway, however, remains elusive. Here, we report transcription targets, independently and dependently, regulated by the calcineurin/NFAT signaling during the E13.5-E16.5 myocardium transition. We have uncovered that expression of one-third of the induced genes during myocardium transition is calcineurin/NFAT-dependent. Among these calcineurin/NFAT-dependent transcription targets, there is a dosage-dependent regulation. Molecular studies indicate that formation of distinct NFAT:DNA complex, in part, accounts for the dosage-dependent regulation. Thus, in addition to temporal and spatial regulation, dosage-dependent threshold requirement provides another mechanism to modulate transcription response mediated by the calcineurin/NFAT signaling during heart development.