Genetic modifications of trees may provide many benefits, e.g. increase production, and mitigate climate change and herbivore impacts on forests. However, genetic modifications sometimes result in unintended effects on innate traits involved in plant-herbivore interactions. The importance of intentional changes in plant defence relative to unintentional changes and the natural variation among clones used in forestry has not been evaluated. By a combination of biochemical measurements and bioassays we investigated if insect feeding on GM aspens is more affected by intentional (induction Bt toxins) than of unintentional, non-target changes or clonal differences in innate plant defence. We used two hybrid wildtype clones (Populus tremula x P. tremuloides and Populus tremula x P. alba) of aspen that have been genetically modified for 1) insect resistance (two Bt lines) or 2) reduced lignin properties (two lines COMT and CAD), respectively. Our measurements of biochemical properties suggest that unintended changes by GM modifications (occurring due to events in the transformation process) in innate plant defence (phenolic compounds) were generally smaller but fundamentally different than differences seen among different wildtype clones (e.g. quantitative and qualitative, respectively). However, neither clonal differences between the two wildtype clones nor unintended changes in phytochemistry influenced consumption by the leaf beetle (Phratora vitellinae). By contrast, Bt induction had a strong direct intended effect as well as a post experiment effect on leaf beetle consumption. The latter suggested lasting reduction of beetle fitness following Bt exposure that is likely due to intestinal damage suffered by the initial Bt exposure. We conclude that Bt induction clearly have intended effects on a target species. Furthermore, the effect of unintended changes in innate plant defence traits, when they occur, are context dependent and have in comparison to Bt induction probably less pronounced effect on targeted herbivores.