Hexabromocyclododecane (HBCD) is a flame retardant that is undergoing environmental risk assessment. The liquid chromatographic retention and electrospray ionization matrix effects were investigated for HBCD methods of analysis for environmental matrices. Column selectivity towards HBCD diastereomers was evaluated for C30 and C18 stationary phases under different mobile phase conditions and column temperatures. The HBCD elution order was dependent on the shape selectivity of the stationary phase and the mobile phase composition. Greater resolution, on columns with reduced shape selectivity, of beta-HBCD and gamma-HBCD was achieved with the use of an acetonitrile/water (compared with a methanol/water) mobile phase composition. A liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method for the analysis of HBCD in biological tissues was evaluated for potential matrix effects. The influence of extracted matrix components on HBCD diastereomer and enantiomer analysis was investigated using a postextraction addition approach. Although the analysis of HBCD diastereomers was relatively unaffected by the sample matrix, the responses of the HBCD enantiomers in tissue samples were significantly influenced by matrix effects and other changes to the ionization conditions. The use of racemic 13C-labeled HBCD diastereomers as internal standards for enantiomer fraction measurements corrected for the changes in the mass spectrometer response.