More than most other animal control techniques, toxic baiting is fraught with the potential impact on non-target species. In the present study, we investigated the effect of aerial baiting with 1080 to control wild dogs in north-eastern New South Wales (NSW), Australia, on populations of southern bush rats (Rattus fuscipes assimilis) and brown antechinus (Antechinus stuartii), using a controlled experiment. Six populations, three each within widely spaced baited and unbaited trapping grids, were monitored before and after bait laying. To develop capture–mark–recapture indices, separate 4-day trapping surveys were undertaken twice before and twice after meat baits (250 g containing 6 mg sodium fluoroacetate, 1080) were delivered from a helicopter at 40 baits per kilometre. To assess non-fatal bait consumption, all baits contained rhodamine B (RhB), which gets incorporated into the vibrissae of animals that have ingested this marker. Neither mammal population decreased in size after baiting, nor was there any increase in population turnover rates or changes in the movement patterns of either species. Furthermore, no trapped animal tested positive for RhB, suggesting that these small mammals rarely consume meat baits, and that, at the population level, the impact of baiting on them was likely negligible. It is therefore unlikely that the current practise of aerial baiting in NSW, although effective in reducing dog activity, threatens populations of these two common species and perhaps small mammals in general.