Abstract Martínez-Gómez, C., Vethaak, A. D., Hylland, K., Burgeot, T., Köhler, A., Lyons, B. P., Thain, J., Gubbins, M. J., and Davies, I. M. 2010. A guide to toxicity assessment and monitoring effects at lower levels of biological organization following marine oil spills in European waters. – ICES Journal of Marine Science, 67: 1105–1118. The usefulness of applying biological-effects techniques (bioassays and biomarkers) as tools to assist in evaluating damage to the health of marine ecosystems produced by oil spills has been demonstrated clearly during recent decades. Guidelines are provided for the use of biological-effects techniques in oil spill pollution monitoring for the NE Atlantic coasts and the NW Mediterranean Sea. The emphasis is on fish and invertebrates and on methods at lower levels of organization (in vitro, suborganismal, and individual). Guidance is provided to researchers and environmental managers on: hazard identification of the fuel oil released; selection of appropriate bioassays and biomarkers for environmental risk assessment; selection of sentinel species; the design of spatial and temporal surveys; and the control of potential confounding factors in the sampling and interpretation of biological-effects data. It is proposed that after an oil spill incident, a monitoring programme using integrated chemical and biological techniques be initiated as soon as possible for ecological risk assessment, pollution control, and monitoring the efficacy of remediation. This can be done by developing new biomonitoring programmes or by adding appropriate biological-effects methods to the existing monitoring programmes.