Chapter 7 Firewall for FortiOS 5.0 : Firewall concepts : FortiGate Modes
  
FortiGate Modes
The FortiGate unit has a choice of modes that it can be used in, either NAT/Route mode or Transparent mode. The FortiGate unit is able to operate as a firewall in both modes, but some of its features are limited in Transparent mode. It is always best to choose which mode you are going to be using at the beginning of the set up. Once you start configuring the device, if you want to change the mode you are going to lose all configuration settings in the change process.