Aims Randomly compare the magnetic navigation system (MNS) to standard guidewire techniques in managing bifurcating lesions. Methods and results Thirty-one consecutive patients with bifurcating lesions were randomized to cross the bifurcating vessels prior to treatment and thereafter the struts of deployed stents with either magnetic or standard guidewires. Crossing success, crossing/fluoroscopy times, and contrast media usage were directly compared. Similar times were noted in both the magnetic wire crossings (median, IQR; 68 s, 45-138 s vs. 59 s, 32-133 s) and fluoroscopic times (median, IQR; 62 s, 44-135 s vs. 55 s, 27-133 s) when compared with standard conventional wires passage through the deployed struts. The MNS successful crossings were 30/31 (96.8%) compared with 28/31 (90.0%) observed with the standard wires. Two previously failed standard wire cases were successfully crossed with magnetic guidewires. Conclusion In contemporary stented bifurcations, the MNS achieved equivalent crossing/fluoroscopy times through deployed stents struts and may be useful in salvaging failed standard wire cases.