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St. John's wort products are commonly standardized to total naphthodianthrones and hyperforin. Determination of these marker compounds is complicated because of the photochemistry of the naphthodianthrones pseudohypericin and hypericin and the instability of hyperforin in solution. Protopseudohypericin and protohypericin have been identified as naturally occurring naphthodianthrones and, when exposed to light, they are converted into pseudohypericin and hypericin, respectively. However, exposure to light and the resulting naphthodianthrone free-radical reactions oxidize hyperforin. A mathematical relationship between the response of the proto compound and the resulting naphthodianthrone can be established by comparing the analytical response of the proto compound in a solution protected from light with the increase in the analytical response of naphthodianthrone in the same solution after exposure to light. By mathematically converting the proto compounds to their respective products, exposure to light can be avoided while still including proto compounds in a single assay. The method presented here details the reporting of all significant naphthodianthrones, including protopseudohypericin and protohypericin, without exposure to light. This approach includes the benefits of improved naphthodianthrone precision and protection of hyperforin from oxidation.