With increasing use of herbal medicines for chronic or serious illness, relevant quality assurance methods are essential for making claims of therapeutic benefit. Adequate demonstration of safety and efficacy based on chemical composition and ensuring consistency between manufactured batches is critical. To date, there has been no uniform standard approach or detailed framework provided to industry for selecting relevant chemical markers used to standardize herbal products. We developed the Herbal Marker Ranking System (Herb MaRS) providing guidance on prioritizing the selection of chemical markers for quality control of complex multi-herb mixtures, while also taking into account the bioactivity in relation to the symptoms of the disease and its concentration in the formula. We apply the Herb MaRS evaluation criteria to a seven-herb formulation for the treatment of irritable bowel syndrome with constipation. Our ranking scale accommodates the clinical and pharmacological use of the formulation and its claimed indications.