Objective Two different Medtronic implantable pulse generator (IPG) models are currently used in clinical applications of deep brain stimulation (DBS): Soletra and Kinetra. The goal of this study was to evaluate and compare the stimulation waveforms produced by each IPG model. Methods We recorded waveforms from a broad range of stimulation parameter settings in each IPG model, and compared them to idealized waveforms that adhered to the parameters specified in the programming device. We then used a previously published computational model to predict the neural response to the various stimulation waveforms. Results The stimulation waveforms produced by the IPGs differed from the idealized waveforms assumed in previous theoretical and clinical studies, and the waveforms differed among the IPG models. These differences were greater at higher frequencies and longer pulse widths, and caused variations of up to 0.4V in activation thresholds for model axons located 3mm from the DBS electrode contact. Conclusions The specific details of the stimulation waveform directly affect the neural response to DBS and should be accounted for in theoretical and experimental studies of DBS. Significance While the clinical selection of DBS parameters is individualized to each patient based on behavioral outcomes, scientific analysis of stimulation parameter settings and clinical threshold measurements are subject to a previously unrecognized source of error unless the actual waveforms produced by the IPG are accounted for.