Pharmacometabolomics may decrease the burden on the healthcare system by better gauging the correct choice of treatment drug and dosage in order to optimize the response of a patient to a treatment. Hopefully, this approach will also ultimately limit the number of adverse drug reactions (ADRs) associated with many treatment regimens. Overall, physicians would be better able to apply more personalized, and potentially more effective, treatments to their patients. It is important to consider, however, that the processing and analysis of the patient samples takes time, resulting in delayed treatment. 
Another concern about the application of pharmacometabolomics analyses to individual patient care, is deciding who should and who should not receive this in-depth, personalized treatment protocol. Certain diseases and stages of disease would have to be classified according to their requirement of such a treatment plan, but there are no criteria for this classification. Furthermore, not all hospitals and treatment institutes can afford the equipment to process and analyze patient samples on site, but sending out samples takes time and ultimately delays treatment. 
Health insurance coverage of such procedures may also be an issue. Certain insurance companies may discriminate against the application of this type of sample analysis and metabolite characterization. Furthermore, there would have to be regulations put in place to ensure that there was no discrimination by insurance companies against the metabolic profiles of individual patients (“high metabolizers” vs. risky “low metabolizers”).