An HVAC controller and/or server may be programmed to determine if ventilation of a building is desired based, at least in part, on the one or more user-specified air quality thresholds stored in a memory, and one or more of a measure of indoor air quality and a measure of outdoor air quality. The air quality parameter threshold may relate to an air quality index, an air pollutant concentration, a smog alert, a pollen count, a dew point, a chance of precipitation, and/or the like. In addition, the HVAC controller and/or server may take into account current or future weather conditions when determining the ventilation needs of a building. Upon determining that ventilation is needed or recommended, the HVAC controller may send or display a message to the user. The message may recommendation that the user open a window or operate a ventilation system, as desired.