The origination of ill-defined layer in organic spin valves was investigated by using atomic force microscopy (AFM) and Rutherford backscattering (RBS) analysis. It was found that conductive bulges of LSMO film and self-grown pinholes in Alq(3) film other than Co inclusions could lead to the formation of ill-defined layer. The morphology of LSMO substrate had a strong influence on that of Alq(3) film, LSMO/Alq(3) and Alq(3)/Co interfaces. Moreover, Alq(3) film with the thickness of 1-4 nm could be barriers which was explained by small active area and added insulated layer in organic magnetic tunnel junctions. (C) 2008 Elsevier B.V. All rights reserved.