We assessed use and selection of cover by coastal cutthroat trout (Oncorhynchus clarkia clarkii) in six headwater streams in three watersheds in western Oregon, USA during the summer low flow period from 1 August and September 30, 2007. We tagged 1037 coastal cutthroat trout (>100 mm) with passive integrated transponder (PIT) tags across all streams. Selection of cover was analyzed by comparing characteristics of locations used for concealment by relocated fish relative to characteristics of randomly available habitat that could be used for concealment. We measured habitat characteristics for 190 relocated individual fish using cover and 797 randomly points potentially available as cover. Of the latter points, only 235 of 797 were potential cover, based on characteristics of cover actually used by fish. Coastal cutthroat trout used substrate as cover (78%) more often than all other cover types combined (22%). Availability of different cover types was variable, but overall substrate made up 92% of available cover and the remaining 8% represented all other cover types combined. Habitat characteristics measured for both used and available cover included depth at fish location (cm), surface area of cover (m2), proximity to depth of 20 cm for fish located in < 20 cm in depth, b-axis (mm) for substrate >2 mm, and distance under substrate. Each of these habitat characteristics was different for used and available cover.