High levels of 3-HPAA in the urine reflect an increased intake of food compounds such as teas, fruits, (orange juice) supplements, particularly quercetin and grape seed extract or possibly a colonic flora population that results in enhanced phenol and flavonoid metabolism.

Higher levels are associated with higher levels of Clostridia. Clostridia bacteria are commonly found in the gut-microbiome. Overuse of antibiotics can cause imbalance of the gut microbiome, leading to overgrowth of the species Clostridioides difficile causing a serious infection. Effects of this infection can lead to severe diarrhea and also the increase in severity of many bowel related diseases is also increased as a results of the infection. Other Clostridia bacteria in the gut have been linked to brain connectivity and healthy function.

3-Hydroxyphenylacetic acid can also be found in Klebsiella. Klebsiella organisms can lead to a wide range of disease states, notably pneumonia, urinary tract infections, sepsis, meningitis, diarrhea, and soft tissue infections.