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Herbicide exposure has been associated with acute poisoning and several chronic diseases. Humans and plants share biological processes targeted by herbicides. Investigating these shared pathways can uncover crucial insights into the underlying mechanisms of herbicides in humans, identify potential biomarkers of herbicide-induced effects, and advance our understanding of related biological processes. The tubulin and key enzymes of metabolic pathways, such as hydroxyphenylpyruvate dioxygenase (HPPD), acetyl-CoA carboxylase (ACC), glutamine synthetase (GS), and protoporphyrinogen oxidase (PPO), have been identified as molecular targets of herbicides in humans. These molecules exhibit relative selectivity for herbicide exposure and can be quantified using well-established techniques, thereby representing potential effect biomarkers. Some of these enzymes play crucial roles in regulating all aspects of the immune response. Furthermore, these shared enzymes, as well as other enzymes involved in plant-specific metabolic pathways that are not present in humans, are found in bacteria and fungi of the gut microbiota, therefore also representing potential targets of herbicides. This study highlights molecular targets of herbicides in humans, which may serve as early indicators of biological changes preceding adverse effects or disease. Some of these enzymes are involved in key steps of the regulation of immune responses, which may thereby be disrupted by herbicide exposure. These targets, along with other plant-specific molecules, are also present in gut microbiota microorganisms, where herbicide exposure may disrupt their function and provide a mechanistic link to intestinal dysbiosis, a condition increasingly associated with chronic diseases.