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In this article, a virtual sensor for the estimation of the injected pilot mass in-cycle is proposed. The method provides an early estimation of the pilot mass before its combustion is finished. Furthermore, the virtual sensor can also estimate pilot masses when its combustion is incomplete. The pilot mass estimation is conducted by comparing the calculated heat release from in-cylinder pressure measurements to a model of the vaporization delay, ignition delay, and the combustion dynamics. A new statistical approach is proposed for the detection of the start of vaporization and the start of combustion. The discrete estimations, obtained at the start of vaporization and the start of combustion, are optimally combined and integrated in a Kalman Filter that estimates the pilot mass during the vaporization and combustion. The virtual sensor was programmed in a field programmable gate array (FPGA), and its performance tested in a Scania D13 Diesel engine.