The primary purpose of clinical Brain Computer Interface (BCI) systems is to help patients communicate with their environment or to aid in their recovery. BCI can be used to replace, restore, enhance, supplement, or improve natural Central Neural System (CNS) output (Wolpaw and Wolpaw, 2012).A common denominator for all BCI patient groups is that they suffer from a neurological deficit. As a consequence, BCI systems in clinical and research settings operate with control signals (brain waves) that could be substantially altered compared to brain waves of able-bodied individuals. Most BCI systems are built and tested on able-bodied individuals, being insufficiently robust for clinical applications. The main reason for this is a lack of systematic analysis on how different neurological problems affect the BCI performance.This special issue highlights interaction of BCI systems with the underlying neurological problems and how performance of these BCI system differ compared to similar systems tested on healthy individuals. The issue presents 4 reviews (Friedrich et al