Butterflies and moths (Lepidoptera) are correlated with many biotic and abiotic characteristics of the environment, and are widely accepted as relevant protection goals. Adverse effects on butterflies and moths through genetically modified (GM) crops have been demonstrated, by both insect-resistant and herbicide-tolerant events. Thus, Lepidoptera are considered suitable bio-indicators for monitoring the potential adverse effects due to the cultivation of GM crops, and guidelines were developed under the umbrella of the Association of German Engineers VDI (Verein Deutscher Ingenieure), entitled “Monitoring the effects of genetically modified organisms (GMO) – Standardised monitoring of butterflies and moths (Lepidoptera): transect method, light trap and larval survey”. Here, the background and rationale of the VDI guidelines is presented, including a summary of the methods described in the guidelines. Special emphasis is given to the discussion of underlying reasons for the selection and adjustment of the applied methodology with respect to the GMO monitoring of day-active Lepidoptera, of night-active moths and of the recording of lepidopteran larvae, as well as to sample design and strategy. Further aspects possibly interfering with monitoring quality are treated such as landscape patterns, low species number and abundance in agro-ecosystems, or high year-to-year fluctuations of populations of Lepidoptera. Though specifically designed for GM crops, the VDI guidelines may also serve as a template to monitor the effects of a wider range of adverse factors on Lepidoptera in agriculture.