A microtracker was a tiny device implanted underneath a person's skin to keep tabs on their movement.
The terrorist ringleader Habib Marwan demanded that CTU Los Angeles arrange a hostage exchange to distract them from one of his operations. When Jack Bauer was turned over to Marwan's men, CTU handed off the young boy Behrooz Araz who had been outfitted with a tracking device in his watch and microtracker below his scalp. Abdullah used a scanner to detect them, and destroyed them both.
Jack Bauer had his TAC team implant a tracking device into Dmitri Gredenko's left arm. This emitted a harmless isotope that was easy to trace. Once Gredenko was in place with his associate Abu Fayed, he alerted them of the device, and Fayed's men chopped off Gredenko's arm.
Later, CTU agent Mike Doyle implanted a tracker inside Josh Bauer, so he could follow Josh and find federal fugitive Phillip Bauer after exchanging Josh for the FB Sub Circuit Board. However, Phillip's mercenaries scanned Josh, discovered the tracker, and disabled it.