The objective of this study was to investigate reliability of transcranial magnetic stimulation (TMS) parameters for three coil systems; hand-held circular and figure-of-eight and navigated figure-of-eight coils. Stimulus response curves, intracortical inhibition (SICI) and facilitation (ICF) were studied in the right first dorsal interosseus muscle of 10 healthy adults. Each coil system was tested twice per subject. Navigation was conducted by a custom built system. Cortical excitability showed moderate-to-good reliability for the hand-held and navigated figure-of-eight coils (Intraclass correlation coefficients (ICCs) 0.55-0.89). The circular coil showed poor reliability for motor evoked potential (MEP) amplitude at 120% resting motor threshold (RMT; MEP(120)) and MEP sum (ICCs 0.09 & 0.48). Reliability for SICI was good for all coil systems when an outlier was removed (ICCs 0.87-0.93), but poor for ICF (ICCs < 0.3). The circular coil had a higher MEP(120) than the navigated figure-of-eight coil (p = 0.004). Figure-of-eight coils can be used confidently to investigate cortical excitability over time. ICF should be interpreted with caution. The navigation device frees the experimenter and enables tracking of the position of the coil and subject. The results help guide the choice of coil system for longitudinal measurements of motor cortex function.