BackgroundAdequate counselling on contraceptive methods can help users choose the most appropriate method. The aim of this study was to assess the effects of structured counselling provided by gynaecologists on selection of a combined hormonal contraception method.MethodsWomen aged 18–40 years (n = 1871) who were considering the use of a combined hormonal contraception method (pill, transdermal patch or vaginal ring) underwent a structured counselling session in which gynaecologists provided comprehensive information. Pre- and post-counselling questionnaires on combined hormonal contraception choice were completed by participants.ResultsAfter counselling, many women (38 %) selected a combined hormonal contraception method that was different from the originally intended one. Preferences for the transdermal patch approximately doubled (from 3.2 % pre-counselling to 7 %; p < 0.0001) and those for the vaginal ring increased four-fold (from 5.2 to 21.2 %; p < 0.0001), while preference for the pill remained unchanged (from 64.5 % [pre-] to 64.1 % [post-counselling]). The proportion of undecided women decreased from 18 to 2.1 % (p < 0.0001). The main reasons for choosing a method were related to ease of use (all methods), and preferences for administration frequency (daily, weekly or monthly). The number of patients requiring post-counselling contact with the physician’s office was low (5.1–6.9 %), as was the incidence of adverse events (1.8–3.1 %).ConclusionsCounselling has a significant impact on women’s choice of combined hormonal contraception and encourages them to consider alternative methods to combined oral contraceptives. Moreover, it also enables women to use their chosen method with confidence.Trial registrationNCT01181778, Trial registration date: August 12, 2010Electronic supplementary materialThe online version of this article (doi:10.1186/s12905-015-0226-x) contains supplementary material, which is available to authorized users.