Abstract. Functional near infrared spectroscopy (fNIRS) is a rapidly developing neuroimaging modality for exploring cortical brain behaviour. Despite recent advances, the quality of fNIRS experimentation may be compromised in several ways. Firstly, by altering the optical properties of the tissues encountered in the path of light. Secondly, through adulteration of the recovered biological signals (noise). And finally, by modulating neural activity. Currently, there is no systematic way to guide the researcher regarding these factors when planning fNIRS studies. Conclusions extracted from fNIRS data will only be robust if appropriate methodology and analysis in accordance with the research question under investigation are employed. In order to address these issues and facilitate the quality control process, a taxonomy of factors influencing fNIRS data have been established. For each factor, a detailed description is provided, and previous solutions are reviewed. Finally, a series of evidence-based recommendations are made with the aim of improving consistency and quality of fNIRS research.