The use of bottom-up fabrication of nanostructures for nanotechnology inherently requires two-dimensional control of the nanostructures at a particular surface. This could in theory be achieved crystallographically with a structure whose three-dimensional unit cell has two or more-tuneable-dimensions on the nanometre scale. Here, we present what is to our knowledge the first example of a truly periodic two-dimensional nanometre-scale phase separation in any inorganic material, and demonstrate our ability to tune the unit-cell dimensions. As such, it represents great potential for the use of standard ceramic processing methods for nanotechnology. The phase separation occurs spontaneously in the homologous series of the perovskite-based Li-ion conductor, (Nd2/3-xLi3x)TiO3, to give two phases whose dimensions both extend into the nanometre scale. This unique feature could lead to its application as a template for the assembly of nanostructures or molecular monolayers.