Genetic variation in G-protein coupled receptors (GPCRs) is associated with a wide spectrum of disease phenotypes and predispositions that are of special significance because they are the targets of therapeutic agents. Each variant provides an opportunity to understand receptor function that complements a plethora of available in vitro data elucidating the pharmacology of the GPCRs. For example, discrete portions of the proximal tail of the dopamine D1 receptor have been discovered, in vitro, that may be involved in desensitization, recycling and trafficking. Similar in vitro strategies have been used to elucidate naturally occurring GPCR mutations. Inactive, over-active or constitutively active receptors have been identified by changes in ligand binding, G-protein coupling, receptor desensitization and receptor recycling. Selected examples reviewed include those disorders resulting from mutations in rhodopsin, thyrotropin, luteinizing hormone, vasopressin and angiotensin receptors. By comparison, the recurrent pharmacogenetic variants are more likely to result in an altered predisposition to complex disease in the population. These common variants may affect receptor sequence without intrinsic phenotype change or spontaneous induction of disease and yet result in significant alteration in drug efficacy. These pharmacogenetic phenomena will be reviewed with respect to a limited sampling of GPCR systems including the orexin/hypocretin system, the beta2 adrenergic receptors, the cysteinyl leukotriene receptors and the calcium-sensing receptor. These developments will be discussed with respect to strategies for drug discovery that take into account the potential for the development of drugs targeted at mutated and wild-type proteins.