Artefacts in recordings of the electroencephalogram (EEG) are a common problem in Brain-Computer Interfaces (BCIs). Artefacts make it difficult to calibrate from training sessions, resulting in low test performance, or lead to artificially high performance when unintentionally used for BCI control. We investigate different artefacts' effects on motor-imagery based BCI relying on Common Spatial Patterns (CSP). Data stem from an 80-subject BCI study. We use the recently developed classifier IC_MARC to classify independent components of EEG data into neural and five classes of artefacts. We find that muscle, but not ocular, artefacts adversely affect BCI performance when all 119 EEG channels are used. Artefacts have little influence when using 48 centrally located EEG channels in a configuration previously found to be optimal.