Toxic compounds may interfere with the genetic constitution of populations, either directly through mutagenic activity, or indirectly via population-mediated processes (i.e. selection, bottleneck). These processes are initiated when toxic compounds reduce the survival and/or fecundity of exposed organisms, either through the accumulation of unfavorable mutations or when they adversely affect the physiology of an organism and/or the environment in which it has to survive. In this review, we describe how the RAPD technique can be applied in an ecotoxicological context, providing information on all direct and indirect routes through which toxicants may affect the genetic structure of populations. Based on RAPD band intensity, gain/loss and band numbers, three major types of RAPD fingerprint analyses are discussed, yielding diagnostic, phenetic and genetic information. Ecotoxicological literature examples demonstrate that, under strictly standardized conditions, the RAPD technique can be a useful tool to preliminary assess toxicological population genetic effects, particularly since this technique is relatively inexpensive and yields information on a large number of loci without having to obtain sequence data for primer design. However, currently only a small fraction of its potential is used in ecotoxicology. Statistical tools and parameters, as used in other RAPD studies, should be applied in ecotoxicological research as well in order to fully exploit the potential of this technique. Finally, due to their random nature, RAPD data often must be considered as preliminary until they are further documented by cloning, sequencing and probing techniques.