A toolbox system for vehicles having a flared section with a fender flare extending outwardly from a side of the vehicle, such as dually pickup trucks and the like. The toolbox system has one or more compartments disposed in the flared section and a door, drawer or other mechanism associated with each of the compartments to allow access to a chamber enclosed by the compartment and to close the compartment. Tools, equipment and other materials can be safely and securely placed in the chamber for transport and storage. Preferably, the contour of the door or drawer corresponds to the contour of the outer wall of the fender flare to substantially maintain the original configuration of the flared section. The toolbox system allows the user to transport and store materials in a manner that protects the materials, does not utilize the rear cargo area and maintains the attractiveness of the vehicle.