The restrictions on the use of legacy flame retardants (FRs) have increased the need of alternative FRs to comply with fire safety legislations. In this study, the feasibility of three different gas chromatography-mass spectrometry (GC-MS) techniques were investigated for the analysis of 102 legacy and alternative FRs including polybrominated diphenyl ethers (PBDEs, n=27), halogenated FRs (HFRs, containing bromine and/or chlorine, n=46), and organophosphorous FRs (OPFRs, n=29). The tested techniques included GC-single MS with (i) electon impact (EI) ionization and (ii) negative chemical ionization (NCI), and (iii) GC-tandem MS (MS/MS) with EI ionization. Out of the tested FRs, 90 could be detected under the used conditions on at least one of the three instrument setups. Later experiments included a selection of these FRs. For the majority of tested PBDEs (5 out of 6) and HFRs (24 out of 26), EI-MS/MS provided the highest detectability (i.e. the lowest detection limits), while for most tested OPFRs (8 out of 13), EI-MS performed better. The influence of matrix components on the analysis of FRs (n=45) was investigated by analyzing a fortified surface water sample with the technique with the lowest selectivity, EI-MS. Both peak enhancement and suppression were observed, and significant correlations between matrix effects and several physico-chemical properties (e.g., retention time and boiling point) were found for PBDEs. In a separate clean-up experiment using natural water spiked with legacy and alternative FRs (n=30), alumina provided the highest mean recovery (90%) in comparison to acidified silica (67%) and Florisil (78%). This study provides new knowledge on analysis of FRs including a wide range of alternative FRs, and it will aid in the efforts of FR monitoring in the environment.