Amylose inclusion complexes were prepared from high amylose cornstarch and hexadecyl- and octadecylammonium chloride. The complexes were applied to paper at concentrations of 2–4%. After drying the papers, a sodium hydroxide solution was applied to convert the complexes to the insoluble amine form, rendering the paper hydrophobic. SEM showed that the complexes were uniformly deposited onto the paper with no visible particles. Increased resistance of papers to water penetration was indicated by an increase in the contact angles of water droplets from not measurable to as much as 113°, and by longer times for total absorption of the droplets. Treated papers also absorbed less water than untreated papers, with the C16 amylose-hexadecylammonium chloride complex providing the greatest water resistance (81.2% less water absorbed than untreated paper). Unlike other technologies widely used for rendering paper hydrophobic, the materials used for this novel method are water soluble, non-toxic, biobased, and biodegradable.