Cost-effective and rigorous risk assessments for chemicals may be based on hazard quotients (HQs): the ratio of a measure of exposure to a substance and a measure of the effect of that substance. HQs have been used for many years in ecological risk assessments for the use of synthetic pesticides in agriculture, and methods for calculating pesticide HQs have been adapted for use with transgenic crops. This paper describes how laboratory methods for assessing the ecotoxicological effects of synthetic pesticides have been modified for the measurement of effects of insecticidal proteins, and how these effect measures are combined with exposure estimates to derive HQs for assessing the ecological risks from the cultivation of insect-resistant transgenic crops. The potential for ecological modeling to inform the design of laboratory effects tests for insecticidal proteins is also discussed.