Despite ongoing efforts, the vertical distribution of aerosols globally is poorly understood. This in turn leads to large uncertainties in the contributions of the direct and indirect aerosol forcing on climate. Using the Global Aerosol Synthesis and Science Project (GASSP) database - the largest synthesised collection of in situ aircraft measurements currently available, with more than 1000 flights from 37 campaigns from around the world - we investigate the vertical structure of submicron aerosols across a wide range of regions and environments. The application of this unique dataset to assess the vertical distributions of number size distribution and cloud condensation nuclei (CCN) in the global aerosol-climate model ECHAM-HAM reveals that the model underestimates accumulation-mode particles in the upper troposphere, especially in remote regions. The processes underlying this discrepancy are explored using different aerosol microphysical schemes and a process sensitivity analysis. These show that the biases are predominantly related to aerosol ageing and removal rather than emissions.