Single-cell microfluidic analysis platforms are powerful tools in the characterization of rare phenotypes that exist as subpopulations and may be hidden by bulk averages. Operating at high throughputs and high concentrations is often necessary for processing large volumes required to isolate these rare populations and obtain statistical relevance. The current challenge of working at high concentrations lies in the inability of systems to perform relevant analysis or separation with high accuracy or purity when the interparticle spacing is reduced beyond the system response time, resulting in coincident events. This work proposes the use of structured channels to control interparticle spacing with an inertial microfluidics platform capable of operating at high throughputs (up to 10,000 particles/sec), high concentrations (1-3 million particles/mL), and with heterogeneous cell populations (16% cell size variation). Local expansion-contraction structures and extended chambers are used in series to induce secondary flows that promote repulsion between neighboring particles reliably (>98%) beyond a 40-µm threshold. This use of passive methods to control spacing presents a more robust alternative to active methods such as squeezing sheath fluid or electric and magnetic field manipulation.