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Spiral microchannels have shown promising results for separation applications. Hydrodynamic particle-particle interactions are a known factor strongly influencing focussing behaviours in inertial devices, with recent work highlighting how the performance of bidisperse mixtures is altered when compared with pure components, in square channels. This phenomenon has not been previously investigated in detail for spiral channels. Here, we demonstrate that, in spiral channels, both the proportion and deformability of larger particles (13 μm diameter) impact upon the recovery (up to 47% decrease) of small rigid particles (4 μm). The effect, observed at low concentrations (volume fraction <0.0012), is attributed to the hydrodynamic capture of beads by larger cells. These changes in particles focussing behaviour directly impede the efficiency of the separation – diverting beads from locations expected from measurements with pure populations to co-collection with larger cells – and could hamper deployment of the technology for certain applications. Similar focussing behaviour alterations were noted when working with purification of stem cell end products.