This paper investigates estimating and testing treatment effects in randomized control trials where imperfect diagnostic device is used to assign subjects to treatment and control group(s). The paper focuses on pre-post design and proposes two new methods for estimating and testing treatment effects. Furthermore, methods for computing sample sizes for such design accounting for misclassification of the subjects are devised. The methods are compared with each other and with a traditional method that ignores the imperfection of the diagnostic device. In particular, the likelihood-based approach shows a significant advantage in terms of power, coverage probability and, consequently, in reduction of the required sample size. The application of the results are illustrated with data from an aging trial for dementia and data from electroencephalogram (EEG) recordings of alcoholic and non-alcoholic subjects. Copyright © 2016 John Wiley & Sons, Ltd.