These notes apply to the ​ATMega328P (Uno etc) using the Arduino IDE and libraries unless otherwise noted.

The 328 has 3 timers:

Timer0 (8 bits)

Used for delay(), millis() and micros(). Don't mess with it.

Timer1 (16 bits)

Not normally used. For simple use, see the ​TimerOne library.

For example:

  Timer1.initialize(1);    // set period to 1us
  Timer1.pwm( 9, 128);     // set to 1/8 duty cycle (128/1024) or 125ns pulse

However, this only works on pins 9 and 10;

Timer2 (8 bits)

Used by e.g. the tone() function.