Background: To explore if stimulus-response (S-R) characteristics of the silent period (SP) after transcranial magnetic stimulation (TMS) are affected by changing the SP definition and by changing data presentation in healthy individuals. This information would be clinically relevant to predict motor recovery in patients with stroke using stimulus-response curves. Methods. Different landmarks to define the SP onset and offset were used to construct S-R curves from the biceps brachii (BB) and abductor digiti minimi (ADM) muscles in 15 healthy participants using rectified versus non-rectified surface electromyography (EMG). A non-linear mixed model fit to a sigmoid Boltzmann function described the S-R characteristics. Differences between S-R characteristics were compared using paired sample t-tests. The Bonferroni correction was used to adjust for multiple testing. Results: For the BB, no differences in S-R characteristics were observed between different SP onset and offset markers, while there was no influence of data presentation either. For the ADM, no differences were observed between different SP onset markers, whereas both the SP offset marker "the first return of any EMG-activity" and presenting non-rectified data showed lower active motor thresholds and less steep slopes. Conclusions: The use of different landmarks to define the SP offset as well as data presentation affect SP S-R characteristics of the ADM in healthy individuals. © 2014 van Kuijk et al.; licensee BioMed Central Ltd.