The black rat is among the world's worst vertebrate pests. Yet very little is known of its impacts or potential impacts on biodiversity in Australian ecosystems. In this paper we examine the impacts of black rats on biodiversity values at North Head, Sydney where a wildlife sanctuary is planned in an area with an abundant black rat population. We examined impacts on three key biodiversity elements considered flagships for the sanctuary concept: the endangered wattle Acacia terminalis, seedlings of which are vulnerable to rat grazing; the nests of small passerine birds which are vulnerable to rat predation; and the endangered population of long-nosed bandicoots Peramales nasuta, vulnerable to competition from black rats. Caging experiments using artificial seedling patches in recently burnt areas showed that rabbits or long-nosed bandicoots rather than black rats were the biggest grazing threat to A. terminalis. Similarly, although rats preyed on experimental artificial nests, nest predation was caused largely by other birds. An intensive trapping study showed a negative spatial relationship between black rats and long-nosed bandicoots at both macrohabitat and microhabitat scales in urban areas, suggesting some avoidance may occur. Thus rat impacts on sunshine wattle and birds nests currently appear to be small in comparison to impacts from other fauna, but an increase in the black rat population may heighten their impacts. It is also possible that black rats affect conservation values not measured here and the negative spatial interaction between black rats and long-nosed bandicoots warrants further investigation.