Fluorinated polyurethanes characterized by a segmented structure, containing hard segments based on 4,4'-methylenebis (phenylisocyanate) (MDI), chain-extender 1,4 n-butandiol (BDO), and soft blocks like perfluoropolyether (PFPE), and poly-epsilon-caprolactone (PCL) were synthesized keeping constant the equivalent ratio among reagents, but varying the experimental conditions. Copolymers show a complex micro- and macrostrucrture with different morphology and calorimetry, similar tensile properties and undistinguishable, but strongly upgraded surface properties. The morphology should be governed by the different fluorine content of the polymeric chains along with the hard segment structure; tensile properties are little influenced by the morphology. All these characteristics are interpreted in terms of polymerization procedure which results to be a key parameter for ruling the composition of the different polymeric chains, due to a very limited mutual solubility of the reagents. Surprisingly, a beneficial effect of the catalyst dibutyltindilaurate for the increase of the reaction kinetics among segregated phases in the reaction mass was observed.