In this study, we further investigate toxicity and disease mechanisms relevant in the context of AD for the Aβ1–42 and AβPP‐BACE1 flies by performing immunohistological and biochemical assays to probe: (a) the extent of neuronal death and protein carbonylation, (b) the gene expression level and distribution of markers of early endosomes and lysosomes and (c) the location of AβPP (and its cleavage products including Aβ1–42) and early endosomes and lysosomes in the fly CNS. This evidence concerns the gene APP and Alzheimer disease.