A simple, fast and specific high performance liquid chromatography separation with an electro-spray ionisation tandem mass spectrometry detection in a negative single reaction ion monitoring scan mode was developed and used for the characterization of Polish honeys according to the content of phenolic acids, including caffeic, chlorogenic, p-coumaric, ferulic, homogentisic, p-hydroxybenzoic and vanillic acids, and flavonoids, i.e., apigenin, genistein, hesperetin, kaempferol, luteolin, rhamnetin, rutin, tricetin and quercetin. Target compounds were isolated and pre-concentrated from the honey matrix by means of the solid phase extraction using Strata X (500mg) cartridges. Analysed honeys did not contain tricetin and genistein. Hesperetin was determined for the first time in heather and linden honeys while rutin in rape honey.