In this paper I explore systematically the relationship between Brain-Computer Interfaces (BCIs) and their human users from a phenomenological and cognitive perspective. First, I functionally decompose BCI systems and develop a typology in which I categorize BCI applications with similar functional properties into three categories, those with (1) motor, (2) virtual, and (3) linguistic applications. Second, developing and building on the notions of an embodied tool and cognitive tool, I analyze whether these distinct BCI applications can be seen as bodily or cognitive extensions. Contrary to some recent philosophical claims, I will argue that, although BCI technology may have the potential to become bodily and cognitive extensions for skilled users, at this stage they are not. And while the electrodes may to a variable degree be transparent and incorporated in the body schema, the BCI system as a whole is not. Moreover, BCIs do not have a functional role characteristic for cognition and are therefore not cognitive extensions. Third, based on concepts from the distributed cognition framework, I give a number of suggestions to improve the interface design of linguistic applications, i.e. BCIs that allow its user to spell words by selecting letters on a screen. These suggestions may result in cognitive extension and would enhance the autonomy and quality of life of its users. In sum, in this paper I develop a typology, analysis and critique on the current philosophical debate on BCIs, thereby providing a richer conceptual understanding of BCI systems which allows me to offer some suggestions for improving the interface design of linguistic applications.