In experimental studies the assigned intervention measures the received intervention if full protocol adherence is achieved, but this is rarely the case in public health. The objective of this study was to estimate the effect of a brief counseling intervention delivered in Swedish dental clinics on tobacco use cessation, taking non-adherence into account. We conducted three secondary analyses. In a per-protocol analysis the experimental counseling delivered as intended was contrasted to usual care (control). In an as-treated analysis individuals were compared according to the counseling components actually received, disregarding randomization. In an instrumental variable analysis the effect of the intervention among those who would always be treated as assigned was estimated. Logistic regression was used to examine the association between tobacco cessation outcomes (seven-day abstinence, three-month abstinence, half-reduction, quit attempts) and the defined exposure to the intervention. Protocol adherence in the intervention group was 73.4%. The per-protocol analysis closely replicated the results of the intention-to-treat analysis, showing a statistically significant effect of the brief counseling on the reduction in tobacco consumption OR -1.81, 95% CI [1.06, 3.07], but no significant effect for other outcomes. In the as-treated analysis, receiving more counseling components compared with no tobacco counseling increased the likelihood of half-reduction. The instrumental variable yielded biased results. We conclude that despite application problems, conducting per-protocol, as-treated and instrumental variable analyses in randomized trials where experimental conditions are not strictly standardized strengthens and puts in context the inference based on intention-to-treat analysis. (C) 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license