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Background Cortical inhibition deficits have been demonstrated in several disorders with deficits in impulsive control (e.g., attention-deficit/hyperactivity disorder [ADHD], tic disorder, Tourette syndrome) by using transcranial magnetic stimulation (TMS). With borderline personality disorder (BPD), we investigated another disorder associated with high impulsivity by TMS. We hypothesized that BPD patients display decreased cortical inhibition and/or increased cortical excitation as assessed with TMS. Methods Different inhibitory and excitatory TMS parameters were investigated in 19 unmedicated female BPD patients and 19 healthy control subjects matched for sex, age, handedness, and body height. Additionally, the results were controlled for ADHD symptomatology. Results A reduced cortical silent period (CSP) duration was found in BPD patients compared with healthy control subjects in the right cortex. Even after controlling for ADHD symptoms, this result remained significant. Conclusions These findings support an association between BPD and cortical inhibition deficits as indexed through TMS. The results are discussed considering basic neurobiological mechanisms that may explain our findings of decreased intracortical inhibition in BPD patients.