The next important factor in setting the context and scope is evaluating the environmental conditions that existed prior to the introduction of the LMO to serve as a bench mark for measuring whether or not any adverse effects have occurred. This is known as establishing a baseline.

In risk assessment, the baseline information describes the conditions existing prior to the introduction of the factor whose potential adverse effect is being assessed. In simplified terms, the baseline for the risk assessment of an LMO is a snapshot of the environment prior to the introduction of an LMO. Baselines can refer, for instance, to a particular environment or health conditions of a population.

The baseline should be established with the aim of having measurable information on any element of the likely potential receiving environment that is considered relevant in assessing the impacts from the introduction of the LMO, including considerations on possible impacts on human health.

In practice, if relevant assessment endpoints or representative species are selected, the baseline data will consist of data that establishes the conditions of these endpoints or species before the introduction of the LMO in question.