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In Nikon’s terminology, CLS and iTTL both frequently refer to the same thing. The two terms are often used interchangeably, even though they stand for different words.
CLS stands for Creative Lighting System and references the entire Nikon wireless flash system. It includes the flashes, cameras, and accessories that all work together in the system.
iTTL stands for Intelligent Through The Lens. The “i” does not mean intelligent in the sense that the flash system is really thinking but rather that the system communicates between the flashes and the camera body with wireless flash pulses. These pulses of light (i.e., preflashes) are used by the camera’s computer to judge brightness, colors, and exposure.
The term “Through The Lens” indicates that the camera body is integral to the operation of the flash system because it meters flash output through the lens. In fact, unless you have an iTTL-compatible camera, you can’t shoot in wireless mode with CLS flashes. When you take a photograph that requires flash, the camera’s matrix metering system analyzes light reflected back from the scene by the preflash, and then quickly makes a flash output decision before it opens up the shutter.