The local structures of ternary alkaline-earth hexaborides (MB6,M=Ca0.5Sr0.5,Ca0.5Ba0.5and Sr0.5Ba0.5) have been analysed using X-ray pair distributionfunction (PDF) analysis, Raman spectroscopy and transmission electronmicroscopy (TEM). The results show significant local deviations from theaverage cubic structure within the boron sub-lattice and support the conclusionthat rapid synthesis processes lead to the formation of coherent nanodomainsover length scales of about 10 nm. Reverse Monte Carlo fitting of the PDFsallows for quantification of the displacement disorder within the boron sub-lattice as a function of sample composition. Detailed Raman spectroscopystudies and high-resolution TEM support the models derived from X-rayscattering. The average magnitude of the static displacement disorder varies bysample composition and positively correlates with the cation radius ratios acrossthe three compositions. The new models form a foundation for futurecomputational and experimental studies aimed at understanding and predictingproperties of hexaborides.