The regulatory framework demands the recording of baseline values to detect GMO effects either prior to the market release of the GMO or in a parallel recording of references. One of the main tasks of General Surveillance is to reveal long-term GMO effects. Variability between varieties, shifts in variety spectra, agricultural practice etc. will cause continuous and long-term changes in ecological characters that are typically influenced by cropping regimes. Moreover, several research data on biodiversity showed that GMO effects were hardly detectable within mid-term periods. In conclusion, the simple comparison of baseline values and GMO-dependent data will rarely provide a clear basis for a decision at short time ranges. Therefore, an effect may not clearly be identified as harmful. It is proposed to focus data analysis on the identification and evaluation of long-term trends and work out regulatory management goals as trigger values for the design of General Surveillance and further decisions of the risk management. Methods on data handling and analysis need to be chosen appropriately.