Man1, an inner nuclear membrane protein, regulates transforming growth factor beta signaling by interacting with receptor-associated Smads. In Man1-deficient (Man1(Delta/Delta)) embryos, vascular remodeling is perturbed by misregulation of Smad activity. Here, we show that Man1(Delta/Delta) embryos exhibit abnormal heart morphogenesis including the looping abnormality. We searched for the molecular basis underlying the heart abnormalities and found that the left side-specific genes responsible for left-right (LR) asymmetry, Nodal, Lefty2, and Pitx2, were expressed bilaterally in the lateral plate mesoderm and that their expression was enhanced significantly in mutants. Notably, Lefty1, a marker for the midline barrier, was maintained in Man1(Delta/Delta) mutants. Crossing Man1(Delta/+) with Nodal hypomorphs (Nodal(neo/+)), in which Nodal signaling in the node is disrupted, to generate double homozygous embryos (Man1(Delta/Delta); Nodal(neo/neo)) revealed that the bilateral Nodal was retained in Man1(Delta/Delta); Nodal(neo/neo) embryos. These results suggest that Man1 regulates LR asymmetry by controlling Nodal signaling in a node-independent manner.