Along with the emerging diagnostic capabilities of pharmacometabolomics, there are limitations introduced when individual variability is looked at. The ability to determine an individual's physiological state by measurement of metabolites is not contested, but the extreme variability that can be introduced by age, nutrition, and commensal organisms suggest problems in creating generalized pharmacometabolomes for patient groups. However, as long as meaningful metabolic signatures can be elucidated to create baseline values, there still exists a possible means of comparison.
Issues surrounding the measurement of metabolites in an individual can also arise from the methodology of metabolite detection, and there are arguments both for and against NMR and mass spectrometry (MS). Other limitations surrounding metabolite analysis include the need for proper handling and processing of samples, as well as proper maintenance and calibration of the analytical and computational equipment. These tasks require skilled and experienced technicians, and potential instrument repair costs due to continuous sample processing can be costly. The cost of the processing and analytical platforms alone is very high, making it difficult for many facilities to afford pharmacometabolomics-based treatment analyses.