This paper presents the development of a complete simulation model for a mechanical in-line injection system feed with diesel, biodiesel, bioethanol fuel blends. The mathematical model is built by using the AVL Boost (TM) Hydsim software, while the required input data is carefully derived by making use of existing data as well as formulas and numerical procedures described in this work. This setup enables relatively efficient formulation and set-up of the mathematical model as well as consistent and reasonably accurate derivation of input data. The derived model is used to simulate the injection processes of various bioethanol-biodiesel and bioethanol-diesel fuel blends. The simulation results are compared to experimental data obtained on a Friedman-Maier type 12H100_h test bed at ambient temperature and several operating regimes. The results show that the compared injection pressure and needle lift histories are generally in a good agreement with the experimental ones. Consequently, the simulation model presented is fast and accurate enough to be engaged in various numerical procedures, ranging from investigations of influences of bioethanol addition to injection system optimization.