Background: A single transcranial magnetic pulse over the motor cortex is known to generate repetitive descending activity along the corticospinal tract. With respect to the origin; the earliest volley is named direct wave and the subsequent activity forms indirect (I) waves. I waves are assumed to originate from corticocortical afferents; they can be modulated by several methods and are practical parameters for evaluating motor cortex excitability. Weak transcranial direct current stimulation (tDCS), which has been widely used in human studies since the early 2000s, is a noninvasive and painless modulatory method for studying cortical excitability. We aimed to investigate the modulatory effects of anodal and cathodal tDCS on I waves of healthy controls, as a component of the motor evoked potential response generator. Materials and Methods: Twelve healthy volunteers were enrolled in the study. One mA tDCS was applied for 10 min and single motor unit (SMU) recording technique was used for the identification of I waves. Two conditions were analyzed for each SMU in both anodal and cathodal current polarities; before tDCS and after tDCS. Separate peristimulus time histograms were constituted for each condition. Total peak duration, early peak latency, early peak duration, and early peak discharge rate were calculated. Results: Total peak duration, early peak latency, and early peak duration did not differ between pre and post tDCS conditions in either polarity. However, I1 peak discharge rate was found to be significantly decreased after cathodal tDCS (P: 0.017) and increased after anodal tDCS (P: 0.003). Conclusion: Our results confirm polarity specific effects of tDCS of the primary motor cortex on I waves. According to our knowledge, this is the first study evaluating modulatory effects of tDCS on I waves using SMU recording technique.