OBJECTIVES: Pharmacogenomic testing can be used to identify ultrarapid metabolizers (UM) of codeine to ensure safe drug dosing in breastfeeding women. The objective of the study was to determine the incremental costs of genotyping in averting neonatal adverse events during maternal pharmacotherapy. METHODS: We performed a cost effectiveness analysis to determine the incremental costs of genotyping to guide codeine use compared to standard care per infant adverse event averted .  The base case was a prenatal patient whose metabolizer status was unknown but who may need to be prescribed codeine-containing analgesics for pain relief after delivery and planned to breast feed her child. Parameter estimates and costs were ascertained from a concurrent clinical study, from the literature and expert opinion. RESULTS: Genetic testing to guide pharmacotherapy for maternal analgesia resulted in a cost of $3400 per adverse event averted or $740 per infant symptom day averted, when compared to standard care.  The results were not sensitive to a number of key variables in one way analysis, namely, cost of genetic testing and the probability of UM in the population.  The results were sensitive to the probability of codeine use in the population and the costs of a hospital admission. This study was limited by a small number of trials from which parameter estimates could be extracted and the very small number of adverse events reported in infants. CONCLUSIONS: Although genotyping to guide pharmacotherapy was not cost saving, the cost to avert an infant adverse event may represent good value for money.  It is not yet known whether implementation would be feasible, however these findings will have implications for new mothers and their health care providers world-wide.