The polybrominated diphenyl ethers (PBDEs), a class of brominated flame retardants (BFRs), are food contaminants of animal origin. Interest in food matrices analysis is growing due to the toxicity of PBDEs and European Commission (EC) recommendation (118/2014/EU). Here we review papers concerning methods of PBDEs analysis while focusing on extraction, clean up, chromatographic separation and detection techniques. The emphasis is put on EC recommendation, the congeners and the efficiency of different detection systems. Some analytical problems caused by differences between low- and high-molecular-mass congener properties, especially the possible limitations of BDE-209 analysis, are discussed. Detection techniques and mass spectrometry (MS) ionization modes applied to PBDE level determination in food of animal origin are compared. The gas chromatography (GC) coupled to high-resolution MS is undoubtedly fit for that purpose, but ion trap MS could be used to PBDEs determination as well. ECD is the most sensitive technique; however, other halogen compounds present in sample may interfere with PBDEs congeners necessitating results confirmation. Moreover, the novel atmospheric pressure chemical ionization (APCI) method applied to GC in tandem with MS places this technique in the top category of the most sensitive techniques which may be used.