This study presents the first use of high-angular resolution electron backscatter diffraction (HR-EBSD) to quantitatively characterise geometrically necessary dislocations in quartz subgrain structures. HR-EBSD exploits cross-correlation of diffraction patterns to measure intragranular misorientations with precision on the order of 0.01° with well-constrained misorientation axes. We investigate the dislocation structures of chessboard subgrains in quartz within samples from the Greater Himalayan Sequence, Nepal. Our results demonstrate that chessboard subgrains are formed primarily from two sets of subgrain boundaries. One set consists primarily of {m}[c] edge dislocations, the other consists primarily of dislocations with Burgers vectors. Apparent densities of geometrically necessary dislocations vary from > 10^13 m−2 within some subgrain boundaries to < 10^12 m−2 within subgrain interiors. The results suggest that at pressures above approximately 10 kbar, chessboard subgrains may form within the α-quartz stability field. Most importantly, this study demonstrates the potential of HR-EBSD as an improved method for analysis of intragranular microstructures in quartz that are used as indicators of deformation conditions.