A method which enables the investigation of the buried interfaces without altering the properties of the polymer films is used to study vertical phase separation of spin-coated poly(3-hexylthiophene) (P3HT):fullerene derivative blends. X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) analysis reveals the P3HT enrichment at the free (air) surfaces and abundance of fullerene derivatives at the organic/substrate interfaces. The vertical phase separation is attributed to the surface energy difference of the components and their interactions with the substrates. This inhomogeneous distribution of the donor and acceptor components significantly affects photovoltaic device performance and makes the inverted device structure a promising choice.