Three diisocyanate units having different linearity and planarity on the basis of the arrangement of constituent aromatic rings are used to synthesize three polyurethanes (PUs) and the effects of the molecular structure of the diisocyanate units on phase separated morphologies of PUs have been studied. The linear and planar diisocyanate unit allows good packing of the hard segments in the hard domain by extensive intersegmental hydrogen bonding, and it forms a well ordered, long hard domain. However, the nonlinear and noncoplanar diisocyanate unit shows a lesser degree of hydrogen bonding in the short hard domain. Strong preferential orientation of the rigid/long hard domains inside a macroscopic grain boundary has been observed with the polarizing optical microscope especially for the PU based on the rigid diisocyanate. It was concluded that the molecular structure of the diisocyanate unit in PU plays an important role in determining the interchain interaction, the detailed phase-separated domain structure, and local domain orientation in each grain boundary. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 890-897, 2011