A method of crystallizing a silicon layer and a method of manufacturing a thin film transistor using the same, the method of crystallizing the silicon layer including forming an amorphous silicon layer on a substrate; performing a hydrophobicity treatment on a surface of the amorphous silicon layer so as to obtain a hydrophobic surface thereon; forming a metallic catalyst on the amorphous silicon layer that has been subjected to the hydrophobicity treatment; and heat-treating the amorphous silicon layer including the metallic catalyst thereon to crystallize the amorphous silicon layer into a polycrystalline silicon layer.