We use atom probe tomography (APT) for resolving nanometer scale compositional fluctuations in Cu2ZnSnSe4 (CZTSe) thin-films prepared by co-evaporation and post-deposition annealing. We detect a complex, nanometer-sized network of CZTSe and ZnSe domains in these films. Some of the ZnSe domains contain precipitates having a Cu- and Sn-rich composition, where the composition cannot be assigned to any of the known equilibrium phases. Furthermore, Na impurities are found to be segregated at the CZTSe/ZnSe interface. The insights given by APT are essential for understanding the growth of CZTSe absorber layers for thin-film solar cells and for optimizing their optoelectronic properties. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4788815