Andean streams drain metal-rich bedrock and are subjected to an extreme altitude gradient, which may create highly selective conditions for life. The aim of the present study was to evaluate the combined effects of metals and altitude on benthic macroinvertebrate community composition in Andean streams. Metal-rich sites were characterized by high metal concentrations and low pH, and high-altitude sites were characterized by high ultraviolet-B radiation and low concentrations of dissolved organic matter. Canonical correspondence analysis indicated that the patterns in faunal composition were best explained by metals followed by altitude, with dipterans and collembolans occurring mostly under harsh conditions of high altitude and high metal levels. Interaction between metals and altitude was most evident at metal-rich sites. It is suggested that in Andean streams, metal leaching from igneous rock and altitude may be important factors confining benthic macroinvertebrate communities, reducing their numbers and changing their composition toward specialized taxa.