Stonehenge is dominated by the large, locally derived sarsen stones which comprise the Outer Sarsen Circle and the Inner Sarsen Trilithon Circle. Lithologically they are a hard form of sandstone called silcrete. Less obvious are the smaller ‘bluestones’ which form the Outer Bluestone Circle and Inner Bluestone Horseshoe. The bluestone assemblage is composed of a variety of lithologies, including dolerite (almost all carrying small, cm scale, white to pink ‘spots’), rhyolites, volcanic tuffs and two different types of sandstone. The majority of the bluestones have been provenanced to the Mynydd Preseli area in west Wales some 200 km west of Stonehenge, and the distinctive spots in the dolerites were crucial evidence in making that link. However, despite the importance of the spots in that provenancing model, which provides evidence for one of the most remarkable feats of Neolithic time in north-west Europe, they have been little studied and are not fully characterized. One reason for this is the fact that they are difficult to study using standard optical microscopy because of the fine grain size of the component minerals. In order to gain a greater understanding of the mineralogy and origin of the spots we have used a range of alternative optical and analytical techniques, including high resolution photomicrography, ‘standard’ electron microscopy (SEM-EDS), automated scanning electron microscopy with linked energy dispersive analysis (automated SEM-EDS) and X-ray diffraction. These investigations, based primarily on samples from Carn Goedog and Carn Meini in the Mynydd Preseli, lead us to conclude that the spots result from a two-stage alteration history involving firstly saussuritization of primary igneous calcium-rich plagioclase phenocrysts/glomerocrysts. The saussuritization was probably a late-stage magmatic event, possibly occurring at ca. 400 °C, and led to the development of the secondary minerals clinozoisite, zoisite, albite and muscovite. Subsequently, the dolerites were affected by regional low-grade metamorphism at ca. 250–300 °C, at the transition from the prehnite-pumpellyite to the greenschist facies. During this metamorphism the background (non-spot) areas of the samples were altered with the development of the secondary minerals chlorite, actinolite, epidote, quartz, titanite and further albite. Interpretation of these data shows that the Carn Goedog sample has a higher percentage of secondary minerals compared to the Carn Meini sample, suggesting that the former shows a higher degree of alteration. Further analyses of dolerite samples from the Mynydd Preseli should provide insight into the potential of the extent of rock alteration in the further refinement of understanding the source or sources of the Stonehenge bluestone dolerites.