It has been well established that polyurethanes exhibit a two-phase micro-structure due to the thermodynamic incompatibility between the soft segments and hard seaments. In this work, we reported the effect of fluorinated side chain attached on hard segment on the phase separation and surface topography of polyurethanes. Two sets of fluorinated polyurethanes, namely, poly(ether urethane)s and poly(carbonate urethane)s containing various amounts of chain extender of fluorinated side chains, were investigated by DSC, XPS, DMA, AFM and FTIR. It was found that the phase separation in both bulk and surface increases in fluorinated poly(carbonate urethane)s and the phase mixing increases in fluorinated poly(ether urethane)s, with increasing amounts of fluorinated side chain. The increased degree of hydrogen bonding between hard segments and soft segments was observed by FTIR for fluorinated poly(ether urethane), which is believed to result in the enhanced phase mixing, and the enhanced association of domains with long-range order (hydrogen bonding) between hard segments was evident for fluorinated poly(carbonate urethane)s, which may correspond to the enhanced phase separation. The result is new and provides direct connection between surface topography and bulk phase separation of polyurethanes. (C) 2004 Elsevier Ltd. All rights reserved.