A method for controlling a ventilation system for the ventilation of an enclosure. The ventilation system includes two or more ventilation units, which each selectively and repeatedly can be controlled to establish an air flow to and/or from the enclosure. The method includes the steps of: determining information regarding operational conditions of one or more of the two or more ventilation units by measuring the air flow through or the pressure differential across the ventilation units, generating operation control data for one or more of the ventilation units from information regarding operational conditions determined for at least one other of the ventilation units, and controlling the operation of one or more of the two or more ventilation units by applying the generated operation control data. The invention further relates to a ventilation system for ventilating an enclosure.