Brain-computer interfaces (BCIs) are an emerging and converging technology that translates the brain activity of its user into command signals for external devices, ranging from motorized wheelchairs, robotic hands, environmental control systems, and computer applications. In this paper I functionally decompose BCI systems and categorize BCI applications with similar functional properties into three categories, those with (1) motor, (2) virtual, and (3) linguistic applications. I then analyse the relationship between these distinct BCI applications and their users from an epistemological and phenomenological perspective. Specifically, I analyse functional properties of BCIs in relation to the abilities (particularly motor behavior and communication) of their human users, asking how they may or may not extend these abilities. This includes a phenomenological analysis of whether BCIs are experienced as transparent extensions. Contrary to some recent philosophical claims, I conclude that, although BCIs have the potential to become bodily as well as cognitive extensions for skilled users, at this stage they are not. And while the electrodes and signal processor may to a variable degree be transparent and incorporated, the BCI system as a whole is not. Contemporary BCIs are difficult to use. Most systems only work in highly controlled laboratory settings, require a high amount of training and concentration, have very limited control options, have low and variable information transfer rates, and effector motions are often slow, clumsy and sometimes unsuccessful. These drawbacks considerably limit their possibilities for transparency and incorporation into either the body schema or cognitive system which is essential for bodily and cognitive extension. Current BCIs can therefore only be seen as a weak or metaphorical extension of the human central nervous system. To increase their potential for cognitive extension, I give suggestions for improving the interface design of what I refer to as linguistic applications.