Purpose Electromagnetic tracking systems (EMTSs) have been proposed to assist the percutaneous renal access (PRA) during minimally invasive interventions to the renal system. However, the influence of other surgical instruments widely used during PRA (like ureteroscopy and ultrasound equipment) in the EMTS performance is not completely known. This work performs this assessment for two EMTSs [Aurora (R) Planar Field Generator (PFG); Aurora (R) Tabletop Field Generator (TTFG)]. Methods An assessment platform, composed by a scaffold with specific supports to attach the surgical instruments and a plate phantom with multiple levels to precisely translate or rotate the surgical instruments, was developed. The median accuracy and precision in terms of position and orientation were estimated for the PFG and TTFG in a surgical environment using this platform. Then, the influence of different surgical instruments (alone or together), namely analogic flexible ureterorenoscope (AUR), digital flexible ureterorenoscope (DUR), two-dimensional (2D) ultrasound (US) probe, and four-dimensional (4D) mechanical US probe, was assessed for both EMTSs by coupling the instruments to 5-DOF and 6-DOF sensors. Results Overall, the median positional and orientation accuracies in the surgical environment were 0.85 mm and 0.42 degrees for PFG, and 0.72 mm and 0.39 degrees for TTFG, while precisions were 0.10 mm and 0.03 degrees for PFG, and 0.20 mm and 0.12 degrees for TTFG, respectively. No significant differences were found for accuracy between EMTSs. However, PFG showed a tendency for higher precision than TTFG. AUR, DUR, and 2D US probe did not influence the accuracy and precision of both EMTSs. In opposition, the 4D probe distorted the signal near the attached sensor, making readings unreliable. Conclusion Ureteroscopy- and ultrasonography-assisted PRA based on EMTS guidance are feasible with the tested AUR or DUR together with the 2D probe. More studies must be performed to evaluate the probes and ureterorenoscopes' influence before their use in PRA based on EMTS guidance., This work has been funded by European Regional Development Funds (FEDER), through the Competitiveness Factors Operational Programme (COMPETE), and by National funds, through the Foundation for Science and Technology (FCT), under the scope of the project POCI-01-0145-FEDER-007038; and by the project NORTE-01-0145-FEDER-000013, supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the FEDER. Joao Gomes-Fonseca and Fernando Veloso were funded by FCT under the Ph.D. grants PD/BDE/113597/2015 and SFRH/BD/131545/2017. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.