Two series of polyurethanes were prepared to investigate the effect of comacrodiol structure on properties and morphology of polyurethanes based on the siloxane macrodiol, alpha,omega-bis(6-hydroxyethoxypropyl) polydimethylsiloxane (PDMS). All polyurethanes contained a 40 wt % hard segment derived from 4,4'-methylenediphenyl diisocyanate (MDI) and 1,4-butanediol (BDO), and were prepared by a two-step, uncatalyzed hulk polymerization. The soft segments were based on an 80/20 mixture of PDMS (MW 967) and a comacrodiol (MW 700), selected from a series of polyethers and polycarbonates. The polyether series included poly(ethylene oxide) (PEO), poly(propylene oxide) (PPO), poly(tetramethylene oxide) (PTMO), poly(hexamethylene oxide), and poly(decamethylene oxide) (PDMO), whereas the polycarbonate series included poly (hexamethylene carbonate) diol (PHCD), poly [bis(4-hydroxybutyl)-tetramethyldisiloxy carbonate] diol (PSCD), and poly [hexamethylene-co-bis(4-hydroxybutyl)-tetramethyldisiloxy carbonate] diol (COPD). Polyurethanes were characterized by size exclusion chromatography, tensile testing, differential scanning calorimetry (DSC), and dynamic mechanical thermal analysis (DMTA). The results clearly demonstrated that the structure of the comacrodiol influenced the properties and morphology of siloxane-based polyurethanes. All comacrodiols, except PEG, improved the UTS of the polyurethane; PHMO and PTMO were the best polyether comacrodiols, while PSCD was the best polycarbonate comacrodiol. Incorporation of the comacrodiol made polyurethanes more elastomeric with low modulus, but the effect was less significant with polycarbonate comacrodiols. DSC and DMTA results strongly supported that the major morphological change associated with incorporation of a comacrodiol was the significant increase in the interfacial regions, largely through the compatibilization with the hard segment. The extent of compatibilization varied with the comacrodiol structure; hydrophilic polyethers such as PEO were the most compatible, and consequently, had poor mechanical strength. Among the polyethers, PHMO was the best, having an appropriate level of compatibility with the hard segment for substantial improvement in mechanical properties. Siloxy carbonate comacrodiol PSCD was the best among the polycarbonates.