Psychological stress affects maternal gastrointestinal (GI) permeability, leading to low-grade inflammation which can impact negatively on fetal development. We investigated a panel of circulating markers as a biological signature of this stress exposure in pregnant women with and without the stress-related GI disorder irritable bowel syndrome (IBS). Markers of GI permeability and inflammation were measured in plasma from healthy (n = 104) and IBS cohorts (n = 105) of women at 15- and 20-weeks' gestation. Biomarkers were evaluated with respect to their degree of association to levels of stress, anxiety and depression as indicated by responses from the Perceived Stress Scale, State-Trait Anxiety Inventory and Edinburgh Postnatal Depression Scale. High levels of stress were associated with elevations of soluble CD14, lipopolysaccharide binding protein (LBP) and tumour necrosis factor-a, while anxiety associated with elevated concentrations of C-reactive protein (CRP) in otherwise healthy pregnancies. Prenatal depression was associated with higher levels of soluble CD14, LBP and CRP in the healthy cohort. High levels of prenatal anxiety and depression were also associated with lower concentrations of tryptophan and kynurenine respectively in the IBS cohort. These markers may represent a core maternal biological signature of active prenatal stress which can be used to inform intervention strategies via stress reduction techniques or other lifestyle approaches. Such interventions may need to be tailored to reflect underlying GI conditions such as IBS.