Herbal and dietary supplement consumption has rapidly expanded in recent years. Due to pharmacological and metabolic characteristics of some supplements, they can interact with prescription medications, potentially leading to clinically important and potentially preventable adverse reactions. Electronic health record (EHR) system provides a valuable source from which drug-supplement interactions can be mined and assessed for their clinical effects. A fundamental prerequisite is a functional understanding of supplement documentation in EHR and associated supplement coverage in major online databases. To address this, clinical notes and corresponding medication lists from an integrated healthcare system were extracted and compared with online databases. Overall, about 40% of listed medications are supplements, most of which are included in medication lists as nutritional or miscellaneous products. Gaps were found between supplement and standard medication terminologies, creating documentation difficulties in fully achieving robust supplement documentation in EHR systems. In addition, in the clinical notes we identified supplements which were not mentioned in the medication lists.