This work was focused on characterization of volatile organic compounds present in honeydew honeys using solid phase microextraction (SPME) followed by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry. Among five commercially available SPME fibres tested for proper sample preparation procedure, divinylbenzene/carboxen/polydimethylsiloxane coating presented the best results as to the total peak areas and higher number of detected compounds. Furthermore, two column setups with diverse orthogonal properties were applied for honeydew honey samples analysis. Consequently, up to 300 compounds were detected at the given signal-to-noise ratio of 200. The identified compounds belonged to various chemical classes (hydrocarbons, alcohols, aldehydes, ketones, terpenes and benzene derivatives). On the basis of the results of the analyses, 2,3-butanediol, 3-hydroxy-2-butanone, acetic acid and methyl ester of 2-hydrobenzoic acid were established as markers of honeydew honey.