Although there is increasing evidence for the effects on wildlife of primary infrastructure (paved roads and human settlements), the effect of secondary infrastructure (tracks and isolated buildings) is generally assumed to be low in sparsely developed areas. We hypothesized that secondary infrastructure may have a negative effect similar to that of primary infrastructure, and hence may be the source of extended impacts in landscapes that are otherwise relatively undisturbed. We studied multi-year breeding site data for a community of large birds (raptors and storks) in the Monfragüe Biosphere Reserve, in the south-west Iberian Peninsula. Using a bootstrap model selection approach we modelled the distribution of breeding sites, using as predictors measures of habitat accessibility (relief, hydrography) and various types of infrastructure (primary and secondary) at different scales. Distance effect functions were developed. Secondary infrastructure exerted a negative effect on breeding sites that was equivalent to that of primary infrastructure, in terms of both transport (track vs road) and dwellings (scattered vs aggregated). The negative effect was distance (rather than density) mediated, and remained within the 1 km scale. The potential impact of secondary infrastructure is greater than that of primary infrastructure as it occupies more extensive areas and includes richer communities, with significant proportions of threatened populations. Our results contradict common assumptions about the negligible impact of secondary infrastructure on biodiversity, reveal new challenges for biodiversity conservation, and provide insights relevant for the spatial planning of isolated buildings and tracks in sparsely developed areas with species of conservation interest.