Transgenic Bacillus thuringiensis (Bt) cotton has had a major impact on the Australian cotton industry by largely controlling lepidopteran pests. However, it also may have other impacts on the invertebrate community that need to be identified. We compared the canopy invertebrate community in sprayed conventional, unsprayed conventional, and unsprayed Bt cotton over three seasons using suction sampling methods. We found that the diversity or species richness of the beneficial communities was reduced in the sprayed crops at two sites. Although spraying had the strongest effect on the community, there was a slight difference between the total community in unsprayed conventional and Bt crops, with crop type accounting for 4.5% of the variance between these communities. Out of over 100 species groups examined, the most consistent differences between unsprayed Bt and conventional communities were higher numbers of Helicoverpa in conventional crops (as would be expected) and slightly higher numbers of Chloropidae and Drosopillidae (Diptera), damsel bugs (Hemiptera, Nabidae), and jassids (Hemiptera, Cicadellidae) in conventional crops. With the advent of Bollgard II and the possibility that 80% of the cotton crop in Australia could be transgenic, the effects of these small differences in the transgenic and conventional communities should be monitored over the long-term to assess if any modifications to cotton management practices need to be made.