Abstract Analytical magnetapheresis is a newly developed technique for analyzing magnetic particles. The magnetically susceptible particles form deposition patterns after flowing through a separation channel in a magnetic field. The separation channel requirements for analytical magnetapheresis are an excellent seal for the carrier flow and ease of disassembly after magnetapheresis. Previously used separation channels often exhibit variable channel leakage and unstable flow velocities. We improved the separation channel assembly to ensure stable, high flow velocities and characterized the system with various magnetically susceptible and labeled particles. Our new separation channel featured silicone sealant with embedded nylon wires and met analytical magnetapheresis requirements. Characterization of this system was performed using several magnetically susceptible particles, and we studied a variety of diamagnetic sample labels with paramagnetic ions and magnetically susceptible particles at different flow-rates and solution pH values. The minimal labeling concentration for complete deposition was determined to be approximately 2.50·10 10 ions per particle for test samples at a flow velocity of 0.67 mm s −1 and a magnetic field gradient of 2.8 T mm −1. Silicas, yeasts and blood cells were used for these studies. We determined that the minimal difference in magnetic susceptibility (Δ χ) for successful separation was approximately 2.00·10 −6 [SI]. The magnetic susceptibilities of Dynabeads M-450 at several separation distances and flow-rates were determined to be 0.25 [SI], within 2% of values published by other workers. The magnetic susceptibilities of various ion-labeled yeasts and cells were determined and most varied by less than 5% at different flow-rates. The results of this study provide very important references for analytical magnetapheresis applications.