The Timer/Counter (TCNT2) and Output Compare register (OCR2) are 8-bit registers. Interrupt request (shorten as Int.Req.) signals are all visible in the Timer Interrupt Flag register (TIFR). All interrupts are individually masked with the Timer Interrupt Mask register (TIMSK). TIFR and TIMSK are not shown in the figure since these registers are shared by other timer units.

The Timer/Counter can be clocked internally, via the prescaler, or asynchronously clocked from the TOSC1/2 pins, as detailed later in this section. The asynchronous operation is controlled by the Asynchronous Status register (ASSR). The Clock Select logic block controls which clock source the Timer/Counter uses to increment (or decrement) its value. The Timer/Counter is inactive when no clock source is selected. The output from the clock select logic is referred to as the timer clock (clkT2).

The double buffered Output Compare register (OCR2) is compared with the Timer/Counter value at all times. The result of the compare can be used by the waveform generator to generate a PWM or variable frequency output on the Output Compare Pin (OC2). For details, see Output Compare Unit. The Compare Match event will also set the Compare flag (OCF2) which can be used to generate an Output Compare interrupt request.