Left-right (LR) asymmetry of the heart in vertebrates is regulated by early asymmetric signals in the embryo, including the secreted signal Sonic hedgehog (Shh), but less is known about LR asymmetries of visceral organs. Here we show that Shh also specifies asymmetries in visceral precursors in the zebrafish and that cardiac and visceral sidedness are independent. The transcription factors fli-1 and Nkx-2.5 are expressed asymmetrically in the precardiac mesoderm and subsequently in the heart; an Eph receptor, rtk2, and an adhesion protein, DM-GRASP, mark early asymmetries in visceral endoderm. Misexpression of shh mRNA, or a dominant negative form of protein kinase A, on the right side reverses the expression of these asymmetries in precursors of both the heart and the viscera. Reversals in the heart and gut are uncoordinated, suggesting that each organ interprets the signal independently. Misexpression of Bone Morphogenetic Protein (BMP4) on the right side reverses the heart, but visceral organs are unaffected, consistent with a function for BMPs locally in the heart field. Zebrafish mutants with midline defects show independent reversals of cardiac and visceral laterality. Thus, hh signals influence the development of multiple organ asymmetries in zebrafish and different organs appear to respond to a central cascade of midline signaling independently, which in the heart involves BMP4.