Transcranial magnetic stimulation (TMS) is useful for modulating neural activity when applied repetitively or assessing neural pathway excitability when applied in single or dual pulse paradigms. TMS devices generate one of two types of stimulus waveforms, monophasic or biphasic, which have dissimilar neuronal activation and therefore different impacts on stimulation effectiveness. Efficacy can be quantified via motor evoked potential (MEP) amplitudes in response to suprathreshold stimuli that represent corticospinal excitability and resting motor thresholds (RMTs), and active motor thresholds (AMT) that represent motor cortical excitability. MEPs vary based on the waveform and direction of the current induced in the brain, being either anterior-to-posterior (AP) or posterior-to-anterior (PA) direction. For instance, studies targeting distal muscles of the upper limb, such as the first dorsal interosseous (FDI), have demonstrated greater efficacy of monophasic stimulation that induces a PA current in the brain relative to biphasic stimulation that induces a PA then AP (biPA-AP) current in the brain by showing reduced RMT with monophasic PA (monoPA) stimulation. The effect of stimulation waveform on TMS metrics have been extensively studied for hand muscles. However, induced current effects on more proximal muscles of the upper limb, such as the biceps brachii, remains to be fully elucidated. Thus, the primary objective of this study was to determine the effect of stimulation type on TMS metrics in the biceps, and in the FDI to provide context of our cohort in light of previous findings. A second objective was to determine the test-retest reliability of TMS metrics for each waveform and muscle. Individuals participated in two sessions. Surface electromyogram (EMG) electrodes were placed over the primary target muscles (biceps and FDI). Maximum voluntary isometric contractions (MVICs) were recorded to normalize MEPs (nMEPs) to the maximum EMG and to determine the AMT during 20% effort. RMT was determined as the lowest stimulus intensity that induced MEPs of ≥ 50 µV in at least 5 of 10 consecutive stimuli with the target muscle fully relaxed. AMT was determined during an isometric contraction of 20 ± 2.5% of their target muscle MVIC as the stimulus intensity that elicited a MEP ≥ 200μV in at least 5 of 10 consecutive stimuli. Ten MEPs were recorded at 120% of RMT for each waveform. TMS stimulation was applied via a Magstim® BiStim² stimulator (monophasic) and Magstim® Super Rapid² Plus¹ stimulator (biphasic), both using a Magstim® D70 Alpha flat (uncoated) coil. RMTs and AMTs were lower for monoPA stimulation compared to biPA-AP stimulation for both the biceps and the FDI, and demonstrated high test-retest reliability. Normalized MEP amplitudes were greater with monoPA than biPA-AP in the FDI, but presented no difference in the biceps. Test-retest reliability of FDI nMEP amplitudes was poor, while moderate reliability was seen in the biceps. This study suggests that current TMS waveform research on upper limb distal muscles is translatable to proximal muscles for motor thresholds but not for MEPs, and test-retest reliability and nMEPs are sensitive to differences in the cortical representations of distal and proximal muscles of the upper limb and lack intermuscular reliability. While further research is needed to elucidate the effect of these two waveforms, this study provides a framework for expected TMS metrics in distal and proximal muscles of the upper limb.