The Convention on Long-Range Transboundary Air Pollution (CLRTAP) has a history covering about thirty years. Over time, NGOs, international and national, environmental, commercial and industrial, have had various degrees of impact on preparations for and the negotiations of its seven substantive Protocols. A special case is the role of science in the CLRTAP process. Can scientific communities or small groups of scientists that have been involved be characterized as NGOs? The answer depends on their roles in the different groups and task forces established under the CLRTAP. This article argues that NGO influence has been more important at the national level in the democratic processes leading to the development of national positions than in their influence during the actual international negotiations. The main influence of NGOs lies in making policy makers aware of environmental problems. There are limitations to NGO participation in the intergovernmental negotiation process, although the scientific NGO input has become a necessary element and strongly influences negotiation outcomes. NGO development towards science has also created an interdependence between the scientific community and policymakers.