Man1, an inner nuclear membrane protein, regulates transforming growth factor β signaling by interacting with receptor-associated Smads. In Man1-deficient (Man1Δ/Δ) embryos, vascular remodeling is perturbed by misregulation of Smad activity. Here, we show that Man1Δ/Δ 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 Man1Δ/Δ mutants. Crossing Man1Δ/+ with Nodal hypomorphs (Nodalneo/+), in which Nodal signaling in the node is disrupted, to generate double homozygous embryos (Man1Δ/Δ; Nodalneo/neo) revealed that the bilateral Nodal was retained in Man1Δ/Δ; Nodalneo/neo embryos. These results suggest that Man1 regulates LR asymmetry by controlling Nodal signaling in a node-independent manner. Developmental Dynamics 237:3565–3576, 2008. © 2008 Wiley-Liss, Inc.