Abstract: Provided are biomarkers for parenteral nutrition associated cholestasis (PNAC) in subjects, especially infants receiving parenteral nutrition (PN). Using such biomarkers provide methods of diagnosing and/or assessing risk of PNAC in a subject, including screening a sample from a subject believed to be at risk for PNAC for one or more biomarkers of PNAC. The biomarkers can include one or more fecal metabolites. Such biomarkers and associated methods provide neonatal intensive care unit clinicians with an additional tool for early identification of PNAC risk. Early identification of high-risk infants would enable clinicians to confidently optimize caloric nutrition with PN for infants at low risk of developing PNAC and enable proactive mitigation with alterations to the administered PN.