A near infrared spectroscopic (NIRS) method is established for quantitative determination of naphthodianthrones and phloroglucine derivatives in St. John's Wort extracts. The validated NIRS method is compared with optimised liquid chromatography (LC) and capillary electrophoresis (CE), applying UV as a detection tool. Optimisation of stationary and mobile phase conditions in reversed-phase liquid chromatography (RP-LC) allow separating the derivatives of interest with high peak symmetry and robustness. Elution takes 15 and 25min on non-porous or porous silica C18 with different porosities, respectively. Capillary electrophoresis (CE) is used for cross-validation of RP-LC. CE enables baseline separation of hypericine and pseudohypericine in less than 2min, but is ten times less sensitive. The validated RP-LC is chosen as a reference method for calibration of the NIRS-system. Analysis of 80 St. John's Wort extracts (320 NIR spectra) and the subsequent chemometric calculations of the best regression model show that NIRS is suitable for analysis of hypericine, pseudohypericine and hyperforine. RP-LC or CE must be employed for the other remaining lower concentrated naphthodianthrone and phloroglucine derivatives. Hypericine and hyperforine are analysed via NIRS with a standard error of estimation (SEE) of 0.52 and 0.50μgmL −1 and standard error of prediction (SEP) of 0.64 and 0.71μgmL −1 within few seconds. The current study demonstrates the suitability of NIRS as an alternative to LC and CE for St. John's Wort producing phytopharmaceutical industry. The short analysis time of few seconds’ assures high sample throughput in routine analysis.