This study investigates particle size reduction and interparticle agglomeration in clear and milky quartz ground in a planetary ball mill for up to 32 h. Particle size distribution and specific surface area were assessed using laser scattering and nitrogen physisorption methods. The heterogeneity in size distribution was calculated using the Rosin-Rammler equation. The onset of agglomeration occurred earlier for clear quartz (4 h) than for milky quartz (16 h). The resistance of the agglomerates formed with clear quartz debris against alkaline dissolution was stronger. These differences were discussed considering the population of ultrafine particles, the line broadening of X-ray diffraction patterns and the paramagnetic centers measured by EPR spectroscopy. The increase in peroxy center concentration occurred simultaneously with the onset of agglomeration. Since no difference was found in hardness and fracture toughness, the lower grinding rates of milky quartz was explained by the higher fracture strength of its polycrystalline microtexture.