A system is provided for reducing temperature gradients within a building. For example, temperature gradients between the air temperature measured at a thermostat controlling an HVAC system and the air temperature in one or more rooms of the building can be reduced. A model of the building is created by measuring the temperature gradient between the thermostat and one or more rooms of the building. This model is used to determine the operation of the HVAC system so as to reduce one or more of such temperature gradients.