Micro-structural investigation of polyurethanes (PUs) with different chain structure has been reported. Polarized optical microscopic studies of aliphatic polyurethanes demonstrate the development of micro clusters with increasing hard segment content (HSC) and crystallization. DSC and XRD results support the crystalline and amorphous nature of aliphatic and aromatic PUs, respectively. Self-assembled biphasic morphology is discernible in aliphatic polyurethane while nanometer size domains are observed in aromatic PUs. The dimension of micro-domain has been measured by using AFM and established its size as independent of hard segment content. The self-assembly is greater for higher HSC aliphatic PUs leading to the formation of bigger domain while the meager hydrogen bond formation restricts the domain size of aromatic polyurethanes. Segmented morphology of surface as well as in bulk of aliphatic polyurethanes is evident from SEM and TEM images and grows with increasing HSC. In contrast, homogeneous and amorphous nature has been observed for aromatic PUs. In situ segregation of phases in aliphatic PUs have been captured through light transmittance and optical images which is categorically absent in aromatic polyurethane. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci 120: 3546-3555, 2011