Every Animagus is required to register with the Ministry of Magic at the Animagus Registry. This registration includes revealing one's animal form and one's distinguishing markings. The register is available to the public. The primary reason for registration is to ensure the Animagi do not abuse their abilities, as the Ministry is able to keep track of them. A prime example is that Rita Skeeter was able to get into Hogwarts undetected (despite being banned from Hogwarts grounds by Dumbledore) by transforming into a beetle. Sirius Black was able to escape from Azkaban and infiltrate Hogwarts Castle in his Animagus form, as the Ministry did not take this into account when imprisoning him. Peter Pettigrew managed to fake his death and hide from the rest of the world in his Animagus form, as the Ministry did not take this into account either since it would help them consider the possibility that he was alive; Pettigrew regarded this advantage as an effective disguise to the Dark Lord.

The penalty for failing to register as an Animagus is a sentence in Azkaban, although the length of time is unknown. Rita Skeeter gave up an entire year of writing articles, her main means of livelihood, so that Hermione Granger would not turn her in as unregistered, and consented to writing an article about Harry's account of the night Lord Voldemort was resurrected free of charge at Hermione's request. That suggests a rather lengthy sentence, even though being sent to Azkaban for any length of time is a considerably bad punishment to begin with.

Due to the complexity of the magic involved, the time it takes, and the limited use (for those who are registered) of the ability, Animagi have become very rare. There was a total of seven known registered Animagi in the twentieth century. It is also partially because of this complexity that Animagi are required to register themselves.

The 2579th edition of Transfiguration Today contained a guide to identifying unregistered Animagi.