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We have studied the microstructure of LaNiO(3)-LaAlO(3) superlattices using transmission electron microscopy in combination with electron energy loss spectroscopy. In superlattices grown on non-polar SrTiO(3) substrates, nanometer-sized NiO precipitates form directly at the interface between the substrate and the initial LaNiO(3) layer, while control measurements on polar substrates show no NiO. Because of the drastically different electronic properties of NiO and LaNiO(3), such precipitates can strongly affect measurements on atomically thin LaNiO(3)-based films and multilayers on SrTiO(3). In general, polarity-driven secondary phase formation should be carefully evaluated as a possible consequence of the polarity mismatch at metal-oxide interfaces. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3663568]