The process of the microphase separation leading to an inhomogenous structure of the polyurethanes prepared from poly(butadiene)diol (PBD), 4,4’-diphenylmethane diisocyanate (MDI) and poly(oxypropylene)triol (POPT) has been investigated by synchrotron small-angle X-ray scattering (SAXS). The development of the two-phase structure of the polyurethanes, consisting of microdomains of higher electron density dispersed in the matrix of PBD chains, was revealed. When POPT is not used in the preparation, the interdomain distance does not increase with time and it corresponds to the root-mean-square end-to-end distance of the PBD chains. In the presence of POPT a distinct growth in the microdomain size and interdomain distance is observed. The scattering data are discussed in terms of the modified Percus-Yevick hard sphere model.