An efficient ultra high performance liquid chromatography (UHPLC)-time-of-flight high resolution mass spectrometry (TOF-HRMS) method was elaborated for the determination of hexabromocyclododecane (HBCD) diastereomers in fish samples and compared against UHPLC-Orbitrap-HRMS and UHPLC-triple quadrupole (QqQ) tandem MS (MS/MS) techniques. The TOF-HRMS analyzer was operated at high resolution (>10000 full width at half maximum (FWHM)) with scanning the m/z range from 600 to 700, to achieve picogram quantitation limits. The effects of various operational parameters on the instrumental response were systematically investigated. Evaluation of the influence of sample clean-up procedure steps on signal suppression effect including removal of the matrix components by means of destructive acidic treatment or non-destructive gel permeation chromatography (GPC), and additional Florisil column chromatography step showed that the analytical response of UHPLC-TOF-HRMS system is much more affected by the presence of matrix components in the final extracts in comparison with UHPLC-Orbitrap-HRMS and UHPLC-QqQ-MS/MS systems. The method was robustly validated and used for the analysis of eel (Anquilla anquilla) samples originating from a Latvian lake. UHPLC-TOF-HRMS showed a suitable performance under the optimized conditions: recoveries for three selected diastereomers in the range of 99-116%; repeatability and intermediate precision expressed as relative standard deviation (RSD) in the ranges of 2.3-7.1% and 2.9-8.1%, respectively. The elaborated method achieved instrumental limits of quantification (i-LOQ) of 0.9-4.5pg on column that were suitable for the trace analysis of three HBCD diastereomers, corresponding to the method limits of quantification (m-LOQ) of 7.0-29pgg(-1) wet weight (w.w.). The efficiency of UHPLC-TOF-HRMS method was evaluated by comparing the performance characteristics and analytical data from real samples with the validation data and real sample results obtained by applying UHPLC-Orbitrap-HRMS and UHPLC-QqQ-MS/MS techniques for the analysis of HBCD in the same fish samples. Statistical assessment of the experimental data by means of the Fiedman's test revealed that UHPLC-TOF-HRMS, UHPLC-QqQ-MS/MS and UHPLC-Orbitrap-HRMS techniques produced adequate and similar results regarding the HBCD content in fish samples. The presence of HBCD diastereomers was confirmed in all the analyzed eels at concentrations up to 554pgg(-1) w.w. for total HBCD and a diastereomer pattern typical for aquatic biota was observed with strong predominance of α-HBCD. The UHPLC-TOF-HRMS is an appropriate technique for diastereomer-specific quantification of HBCD content in fish samples.