Abstract Background Polychlorinated biphenyls (PCBs) are a group of environmental persistent organic pollutants, which can be metabolized into a series of metabolites, including hydroxylated metabolites (OH-PCBs) in biota. Nineteen of 209 PCB congeners can form chiral stable isomers. However, atropisomeric determination of the hydroxylated metabolites of these chiral PCBs has never been reported by LC methods. In this work, a novel HPLC-MS method was developed to detect five chiral OH-PCBs (4OH-PCB91, 5OH-PCB91, 4OH-PCB95, 5OH-PCB95 and 5OH-PCB149) using HPLC-MS without a derivatization step. Results The influences of column-type, column temperature, flow rate and ratio of the mobile phase on the atropisomeric separation were investigated in detail. In the final method, calibration curves, based on peak areas against concentration, were linear in a range of 1–100 ng mL^-1 of five chiral OH-PCBs with correlation coefficients ranging from 0.9996 to 0.9999 for all atropisomers of OH-PCBs. The relative standard deviations measured at the 10.0 ng mL^-1 level for atropisomers of five chiral OH-PCBs were in the range of 0.60-7.55% (n = 5). Calculated detection limits (S/N = 3) of five chiral OH-PCBs were between 0.31 and 0.60 ng mL^-1 for all OH-PCB atropisomers. Conclusion This HPLC-MS method was developed to detect chiral OH-PCBs and further successfully applied to measure OH-PCB atropisomer levels and enantiomeric fractions (EFs) in rat liver microsomal samples. The results from LC-MS method were highly consistent with those from GC-ECD method. It is the first time to report these OH-PCB atropisomers detected in microsomes by HPLC-MS. The proposed method might be applied also to detect chiral OH-PCBs in environmental samples and for metabolites of PCBs in vivo.