Polar metabolites resulting from petroleum biodegradation are measured in groundwater samples as TPHd unless a silica gel cleanup (SGC) is used on the sample extract to isolate hydrocarbons. Even though the metabolites can be the vast majority of the dissolved organics present in groundwater, SGC has been inconsistently applied because of regulatory concern about the nature and toxicity of the metabolites. A two-step approach was used to identify polar compounds that were measured as TPHd in groundwater extracts at five sites with biodegrading fuel sources. First, gas chromatography with mass spectrometry (GC-MS) was used to identify and quantify 57 individual target polar metabolites. Only one of these compounds—dodecanoic acid, which has low potential human toxicity—was detected. Second, nontargeted analysis was used to identify as many polar metabolites as possible using both GC-MS and GC×GC-MS. The nontargeted analysis revealed that the mixture of polar metabolites identified in groundwater source areas at these five sites is composed of approximately equal average percentages of organic acids, alcohols and ketones, with few phenols and aldehydes. The mixture identified in downgradient areas at these five sites is dominated by acids, with fewer alcohols, far fewer ketones, and very few aldehydes and phenols. A ranking system consistent with systems used by USEPA and the United Nations was developed for evaluating the potential chronic oral toxicity to humans of the different classes of identified polar metabolites. The vast majority of the identified polar metabolites have a “Low” toxicity profile, and the mixture of identified polar metabolites present in groundwater extracts at these five sites is unlikely to present a significant risk to human health.