In a recent paper, the authors have introduced the windowed linear canonical transform and shown its good properties together with some applications such as Poisson summation formulas, sampling interpolation, and series expansion. In this paper, we prove the Paley-Wiener theorems and the uncertainty principles for the (inverse) windowed linear canonical transform. They are new in literature and has some consequences that are now under investigation. Copyright © 2012 John Wiley & Sons, Ltd.