Since 1982, problems relating to the alkali–silica reaction of concrete structures have been occurring in Japan. To identify the aggregates causing the reaction, the reactivity of Japanese rocks and the distribution of reactive rocks in Japan have been studied. Observations of aggregates in concrete structures affected by the alkali–silica reaction, reaction experiments (chemical method: ASTM C 289, mortar bar method: ASTM C 227) on the aggregates in the affected concrete and rocks collected from quarries and outcrops, and geological investigations on the results have been performed. As a result, reaction products were observed around andesite, rhyolite and shale, and a reaction rim was recognized in andesite, rhyolite, sandstone, shale and chert. Deleterious and potentially deleterious rocks defined by the chemical method in concrete, which were affected or possibly affected by the alkali–silica reaction, were porphyrite, andesite, dacite, rhyolite, sandstone, shale and chert. The results of the chemical and mortar bar methods on the rocks from quarries and outcrops indicated the same results as the aggregates in concrete structures; the reactive rocks were basalt, andesite, dacite, rhyolite, sandstone, shale, slate, tuffs, chert and quartz schist. The reactivity of volcanic rocks is controlled by the presence of cristobalite, tridymite and volcanic glass. The presence of these minerals is affected by the formation age of the rocks; pre-Miocene rocks do not have reactivity. Reactivities of sedimentary and metamorphic rocks are controlled by crystallinity and content of quartz.