Research in the field of physiotherapy creates some controversy. This article seeks to explore and find out the solutions for this issue. Two aspects are discussed: the difficulties in reconciling the specificity of physiotherapy research with methodological standards and the concerns related to patients’ participation in the research. These problems affect the physiotherapists involved in the creation of ethically and methodologically valuable research project. Physiotherapists conducting research struggle to reconcile two sets of values: the role of a researcher and the role of a professional helper. This article discusses the possibility of creating a valuable research project based on the methodological standards within EBM paradigm in relation to the practical aspects of physiotherapy, such as therapy effectiveness and patient-therapist interaction.