This review contains a description of a research program for the study of maladaptation, defined here in terms of deviation from adaptive peaks. Maladaptation has many genetic causes, including mutation, inbreeding, drift, gene flow, heterozygote advantage and pleiotropy. Degrees of maladaptation are determined by genetic architecture and the relationship between the rates of selective, environmental change and the nature and extent of genetic responses to selection. The empirical analysis of maladaptation requires: (1) recognition of putative maladaptation, using methods from phylogenetics, teleonomy, development and genetics, followed by an assessment of the nature and degree of deviation from adaptation, using studies of natural selection and teleonomy; (2) determination of the causes of the deviation, using analyses of genetics, development, or other methods. Conditions for unambiguously identifying maladaptation are considerably more stringent than those for demonstrating adaptation and remarkably few studies have clearly identified and characterised maladaptative traits. A thorough understanding of the nature of phenotypic variation will never be achieved without an analysis of the scope and usual causes of maladaptation.