This article deals with the validation of and first measurements with a newly constructed flowing afterglow selected ion flow tube (FA-SIFT) instrument. All reactions were studied in He buffer gas at a pressure of 1.43 hPa and a temperature of 298 K. The validation consisted of the study of the gas-phase ion/molecule reactions of methanol and ethanol (M) with the reactant ions H3O+·(H2O)n (n = 0-3), MH+, M2H+, and MH+·H2O and the reactions of MH+ with H2O. Obtained results are compared with available literature data and with calculated collision rate constants. The validated FA-SIFT has subsequently been used to characterize the reactions of the unsaturated biogenic alcohols 2-methyl-3-buten-2-ol, 1-penten-3-ol, cis-3-hexen-1-ol and trans-2-hexen-1-ol (ROH) with H3O+·(H2O)n (n = 0-3) as well as the secondary reactions of the H3O+/ROH product ions with H2O (hydration) and ROH in view of their accurate quantification in ambient air samples with medium-pressure chemical ionization mass spectrometry (CIMS) instrumentation using H3O+ reactant ions. Whereas water elimination following proton transfer was found to be the main mechanism for all H3O+/ROH reactions studied and for the H3O+·H2O/trans-2-hexen-1-ol reaction, all other H3O+·(H2O)n/ROH (n = 1, 2) reactions proceeded by multiple reaction mechanisms. H3O+·(H2O)3 reactions proceeded mainly (C6 alcohols) or exclusively (C5 alcohols) by ligand switching followed by water elimination. Hydration of the H3O+/ROH product ions was observed whenever they contained oxygen. The secondary reactions with ROH were also found to proceed by multiple reaction pathways. © 2009 Elsevier B.V. All rights reserved.