The volatile fraction of Ophrys sphegodes Mill. subsp. sphegodes, Ophrys bertolonii subsp. benacensis (Reisigl) O. Danesch, E. Danasch & Ehrend. and Neotinea tridentata (Scop.) R.M. Bateman, Pridgeon & M.W. Case, three orchid species with different pollinator attraction strategies, sampled in vivo and in situ, were evaluated by headspace solid phase microextraction coupled with gas-chromatography and mass spectrometry. The results were compared with the volatile compounds emitted by flowering plant samples picked from the same populations of orchid species. Hydrocarbons, aldehydes, alcohols and terpenes were the major constituents of “in vivo” orchid scents and some distinctive differences in volatile metabolite composition were observed between Ophrys and Neotinea species. Moreover, the odour bouquets of the picked flowering plant samples were different from the in vivo ones and in particular different proportions of the various terpenes and an increase of α-pinene were observed. In conclusion HS/SPME GCMS proved to be a suitable technique for analyzing and distinguishing the volatile fingerprint of different orchid species, sampled in vivo and in situ in a non-disruptive way, with potentially great advantages for ecophysiological studies of rare and endangered species.