Two novel waterborne polyurethanes containing short fluoroalkyl groups [CH(CF3)2 and CH2CF2CF3] were designed and synthesized. They were applied as surface modification agents on cotton fabrics. The treated cotton fabrics showed good water-repellent properties, and the contact angles for water were 146° for the fluorinated polyurethane with the CH2CF2CF3 group and 132° for the fluorinated polyurethane with the CH(CF3)2 group. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008