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Measuring rail system crowding is important to transit agencies. Crowding data has implications for safety, operations control, service planning, performance measurement, and customer information. This paper proposes a bi-level regression model that transit agencies can use to estimate the number of passengers left behind on a platform by high-frequency trains operating at capacity. Inputs to the model include the number of passenger arrivals between trains and train departure times, which are derived from automatic fare collection and vehicle location data. The data are used to calculate the proposed measure of cumulative capacity shortage, which is shown to have high correlation with the number of passengers left behind. A bi-level regression approach is introduced and applied to calibrate the model parameters based on manual counts of passengers left behind. A case study using data from the Chicago …