Most mutations with observable phenotypic effects are deleterious. Stu
dies of Drosophila and inbred plant populations suggest that a new ind
ividual may have a mean number of new deleterious mutations that excee
ds one-half. Most of these have relatively small homozygous effects an
d reduce fitness by 1-2% when heterozygous. Several striking features
of present-day organisms have apparently evolved in response to the co
nstant input of deleterious alleles by recurrent mutation. For example
, the adaptations of hermaphroditic organisms for outcrossing have bee
n widely interpreted in terms of the benefits of avoiding the reduced
fitness of inbred progeny, which is partly due to deleterious mutation
s. Population genetic models of modifiers of the breeding system in th
e presence of genome-wide deleterious mutation are reviewed and their
predictions related to genetic and comparative data. The evolution of
degenerate Y chromosomes is a phenomenon that may be caused by the acc
umulation of deleterious mutations. The population genetic mechanisms
that can drive this degeneration are reviewed and their significance a
ssessed in the light of available data.