Neonicotinoid insecticides are an important contribution to plant protection products. At the same time, their environmental impact on non-target organisms is often problematic. It has been shown that the toxicity of formulations of neonicotinoid insecticides can originate from non-neonicotinoid additives. In the present study we used chemogenomics to analyse side effects of purified neonicotinoids, additives and formulations on the genome-wide scale. We show that the additives in formulations have more pronounced effects than the active components, and that these effects could explain previously observed negative effects of neonicotinoid insecticides on spermatogenesis in animals. We also demonstrate that cell wall organization and biogenesis in yeast is negatively affected by neonicotinoid substances.