The spread of intelligent buildings and advanced HVAC systems controls emphasizes the necessity of evaluating the impact of malfunctions caused by errors in the design, installation, or maintenance of these systems. In this work, the effect of the most diffused faults in ventilation systems is studied for an air handling unit installed in a Danish residential apartment. For this purpose, a dynamic model was built in Modelica, representing the building and the ventilation system. Different faults with varying intensities were implemented in the model. The impacts were evaluated by comparing the results of the obtained “with-fault” models with the “fault-free” model used as a benchmark. The comparison involved thermal and electrical energy use, thermal comfort and indoor air quality. Results showed that, for the studied system, the increase in thermal energy use was significant for the offset of the sensor controlling the bypass (up to + 27%), the bypass damper leakage and stuck (up to + 90%) and ducts’ thermal losses (up to + 48%). In the latter case, an increase in thermal discomfort was observed (+7% of hours with operative temperature below 18.5 °C).