This two-day workshop brought together regulators and industry and academic scientists from various disciplines to discuss and evaluate current knowledge and research on secondary effects of transgenes that function as transcription factors, in signal transduction, or to modify metabolic pathways. The workshop focused on examples and commercially-promising case studies to promote information exchange and discussion of data and experiments on secondary effects of these genes. We sought to evaluate the information that is available and to identify areas that would benefit from additional research. In particular, secondary effects that could alter confinement, including the propensity for gene flow to wild populations and adjacent, nontransgenic crops, were discussed. The collective knowledge and insight coming from this workshop should be valuable to those who develop these products for commercial purposes and to those who make regulatory decisions on field testing criteria of future transgenic plants.