Twenty caves located in a high altitudinal quartzite area in Brazil were examined for invertebrate richness and composition and in terms of environmental factors that determine community structure. We evaluate how distance, altitude, cave extension, environmental stability, number and size of cave entrances and stream presence can act on species composition and richness. The caves presented a high richness of troglophilic (463 spp.) and troglobitic species (6 spp.) in relation to other siliciclastic caves around the world. The average richness was 39.55 species per cave (sd = 21.87), the quantitative similarity among caves was 41% and turnover was βrepl. = 0.769. Araneae (20% of the sampled species), Diptera (18%) and Coleoptera (14%) were the dominant orders regarding species richness. Only twenty percent of the caves were placed out of the confidence interval of the average taxonomic distinctness (∆+); however, the ∆+ decreased with the increase of environmental stability. Cave extension and stream presence were the main factors determining the variation of species composition among caves. Cave extension also influenced species richness variations. Furthermore, the total richness and richness of troglobitic species increased with cave extension. The threats to these habitats further revealed that the fauna is at risk due to tourism, trampling and natural soil erosion that can promote microhabitat alterations. Therefore, quartzite caves also require special attention regarding conservation actions in order to keep their natural biological dynamics.