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Modulation of the effective compression ratio, a measure of the amount of compression of in-cylinder gases above intake manifold conditions, is a key enabler of advanced combustion strategies aimed at reducing emissions while maintaining efficiency, and is directly influenced by modulation of intake valve closing time. To date, the effective compression ratio has most commonly been calculated from in-cylinder pressure data, requiring reliable in-cylinder pressure sensors. These sensors are generally not found on production engines, and thus a method is needed to determine effective compression ratio without in-cylinder pressure data. The work presented here outlines an estimation scheme that combines a high-gain observer with a physically-based volumetric efficiency model to estimate effective compression ratio using only information available from stock engine sensors, including manifold pressures and temperatures and air flows. The estimation scheme is compared to experimental engine data from a unique multi-cylinder diesel engine test bed with flexible intake valve actuation. The effective compression ratio estimator was tested transiently at five engine operating points and demonstrates convergence within three engine cycles after a transient event has occurred, and exhibits steady-state errors of less than 3%.