Ancient asexuals – organisms that have lived without sex for millions of years – offer unique opportunities for discriminating among the various theories of the maintenance of sex. The last few years have seen molecular studies of a number of putative ancient asexual lineages, including bdelloid rotifers, Darwinulid ostracods, and mycorrhizal fungi. To help make sense of the diverse findings of such studies, we present a review and classification of the predicted effects of loss of sex on the eukaryotic genome. These include: (1) direct effects on the genetic structure of individuals and populations; (2) direct effects on the mutation rate due to the loss of the sexual phase; (3) decay of genes specific to sex and recombination; (4) effects of the cessation of sexual selection; (5) dis-adaptation due to the reduced efficiency of selection; and (6) adaptations to asexuality. We discuss the utility of the various predictions for detecting ancient asexuality, for testing hypotheses of the reversibility of a transition to asexuality, and for discriminating between theories of sex. In addition, we review the current status of putative ancient asexuals. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society 2003, 79, 69–84.