The aggregation of casein micelles (CMs) induced by milk-clotting enzymes is a process of fundamental importance in the dairy industry for cheese production; however, it is not well characterized on the nanoscale. Here we enabled the monitoring of the kinetics of aggregation between single CMs (30-600 nm in diameter) by immobilizing them on a glass substrate at low densities and subsequently imaging them with fluorescence microscopy. We validated the new method by a quantitative comparison to ensemble measurements of aggregation. Single-particle statistics allowed us to observe for the first time several heterogeneities in CM aggregation. We observed two types of CM growth: a slow increase in the size of CMs and a stepwise increase attributed to interactions between aggregates preformed in solution. Both types of growth exhibit a lag phase that was very heterogeneous between different CMs, suggesting significant differences in their composition or structure. Detailed size histograms of CMs during aggregation also revealed the presence of two distinct subpopulations with different growth amplitudes and kinetics. The depedence of these distinct nanoscale processes/parameters on aggregation conditions is not accessible to bulk measurements that report only ensemble-average values and may prove important to an in-depth understanding of CM aggregation.