The chemical compositions of defective regions in microcrystalline thin film Si solar cells are studied using energy-dispersive X-ray spectroscopy and electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope. Nanometer-resolved chemical analysis reveals the presence of ZnO in micrometer-long defective regions. Due to the recent application of unmixing algorithm to EELS, the chemical compositions of the defective regions are determined objectively, without introducing artefacts from the fitting procedures. It is shown that the defective regions in the Si layer are filled by ZnO, which diffuses along voids that propagate from the bottom up to the top ZnO contacts. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4800569]