We study spinodal phase separation in unstable thin liquid films on chemically disordered substrates via simulations of the thin-film equation. The disorder is characterized by immobile patches of varying size and Hamaker constant. The effect of disorder is pronounced in the early stages (amplification of fluctuations), remains during the intermediate stages and vanishes in the late stages (domain growth). These findings are in contrast to the well-known effects of quenched disorder in usual phase-separation processes, viz. the early stages remain undisturbed and domain growth is slowed down in the asymptotic regime. We also address the inverse problem of estimating disorder by thin-film experiments. © 2010 the Owner Societies.