Highly ordered arrays of nanoscale magnetic structures form the basis of artificial spin ices, uniform particles for bio-medical applications, and data storage as Bit Patterned Media. We demonstrate that small-angle X-ray scattering (SAXS) allows the size distribution and the positional alignment of highly ordered arrays to be determined with high spatial and statistical accuracy. The results obtained from the SAXS measurements are compared to an analysis of Scanning Electron Microscopy images and found to be in excellent agreement. This confirms the validity of the technique and demonstrates its potential as a fast, accurate, and statistically reliable method for characterising arrays of ordered nanostructures.