Co-registration of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) is a new, promising method for assessing cortical excitability and connectivity. Using this technique, a TMS evoked potential (TEP) can be induced and registered with the EEG. However, the TEP contains an early, short lasting artifact due to the magnetic pulse, and a second artifact, which depends on the location of stimulation and can last up to 40 ms. Different causes for this second artifact have been suggested in literature. In this study, we used principal component analysis (PCA) to suppress both the first and second artifact in TMS-EEG data. Single pulse TMS was applied at the motor and visual cortex in 18 healthy subjects. PCA using singular value decomposition was applied on single trials to suppress the artifactual components. A large artifact suppression was realized after the removal of the first five PCA components, thereby revealing early TEP peaks, with only a small suppression of later TEP components. The spatial distribution of the second artifact suggests that it is caused by electrode movement due to activation of the temporal musculature. In conclusion, we showed that PCA can be used to reduce TMS-induced artifacts in EEG, thereby revealing components of the TMS evoked potential.