Microchipping provides essential identification that facilitates reunification of lost pets with owners, but the procedure causes momentary pain and the chips themselves carry rare but real complications including migration and infection.
Microchipping involves a momentary welfare cost — the injection pain — in exchange for a lifetime benefit of improved chances of reunification if lost. The welfare calculus strongly favors chipping: the brief pain is comparable to vaccination, while the alternative of losing a pet permanently causes prolonged suffering. Complications are rare and generally treatable. The procedure is one of the clearest examples of a small, acute welfare cost with large, long-term welfare benefits for companion animals.