Context.Habitat degradation and fragmentation of vegetation can transform and deplete local wildlife populations, and is a key threatening process globally. In northern Australian tropical savannas, clearing is relatively rare across the biome, although it is slowly intensifying as a result of increasing agricultural development. However, the terrestrial vertebrates in these largely intact landscapes are undergoing current population declines because of a variety of land-management changes, one of which is increasing land clearing; therefore, there is a need to understand the relative effect of small-scale land clearing the fauna.Aims. The present study examined the variation in abundance of birds, mammals and reptiles in intact, thinned and cleared Eucalyptus woodlands in a tropical savanna bioregion.Methods. The vertebrate fauna were sampled in 88 sites over two general geographic locations within the Desert Uplands in 2005 and 2006. Standardised 1-ha surveys were employed in a single vegetation type and across three treatments. As two discrete locations were examined, linear mixed models were used in the analysis.Key results. The fauna composition varied significantly across the intact, thinned and cleared sites. Bird species richness reduced from intact to thinned and cleared sites, and reptile richness and abundance declined in cleared sites, but was largely unaffected by thinning. Seventeen bird species recorded significant variation in abundance across the three vegetation structural types, with 12 most abundant in the intact sites. Mammals on the whole were recorded in very low abundances and in few sites. For reptiles, two were most abundant in thinned sites and three in intact sites.Conclusions. In the present study, we have demonstrated that small-scale clearing and vegetation manipulation via thinning, even within largely intact tropical savanna woodland, can cause localised depletion of some species, although most notably where the vegetation disruption was most severe (i.e. clearing). Birds are most affected, and many species that declined in abundance are the same as those that suffered severe population reductions as a result of broad-scale clearing in south-eastern Australia.Implications. The proposed increase in the intensity of agricultural land use in northern Australia will result in incremental landscape change as a result of clearing. Understanding how the gradual reduction of vegetation cover and habitat will change the faun assemblage is important for pre-emptive conservation planning. This is vital to avoid the mistakes of extensive landscape change in southern Australia that has left a legacy of a permanently depleted fauna.