The concentrations of l-tryptophan (Trp) and the metabolite l-kynurenine (KYN) can be used to evaluate the in-vivo activity of indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO). As such, a novel method involving derivatization of l-Trp and l-KYN with (R)-4-(3-isothiocyanatopyrrolidin-1-yl)-7-(N,N-dimethylaminosulfonyl)-2,1,3-benzoxadiazole (DBD-PyNCS) and separation by high-performance liquid chromatography (HPLC) with tandem mass spectrometric (MS/MS) detection on a triazole-bonded column (Cosmosil HILIC®) was developed to determine their concentrations. The optimized mobile phase, CH3 CN/10 mm ammonium formate in H2 O (pH 5.0) (90:10, v/v) eluted isocratically, resulted in satisfactory separation and MS/MS detection of the analytes. The detection limits of l-Trp and l-KYN were approximately 50 and 4.0 pm, respectively. The column temperature affected the retention behaviour of the Trp and KYN derivatives, with increased column temperatures leading to increased capacity factors; positive enthalpy changes were revealed by van't Hoff plot analyses. Using the proposed LC-MS/MS method, l-Trp and l-KYN were successfully determined in 10 μL human serum using 1-methyl-l-Trp as an internal standard. The precision and recovery of l-Trp were in the ranges 2.85-9.29 and 95.8-113%, respectively, while those of l-KYN were 2.51-16.0 and 80.8-98.2%, respectively. The proposed LC-MS/MS method will be useful for evaluating the in vivo activity of IDO or TDO. Copyright © 2016 John Wiley & Sons, Ltd.