Secret locations

The Secret Locations in Assassin's Creed II and Assassin's Creed: Brotherhood are Prince of Persia-like platform levels that must be completed through free running and some puzzle solving. These missions are optional, however, the first one must be completed in order to discover a Templar conspiracy against the Medici.

Each location has several stages, and each one has a different platforming objective, from climbing high towers on the inside, to timed free running trials meant to test a player's abilities. Six secret locations are also Assassin's Tombs that contain Seals necessary to unlock Altaïr's Armor, which is the most powerful armor in the game, and is needed for Desmond to achieve full synchronization with Ezio. The first Assassin Tomb (the secret location mentioned in the first paragraph) does not count as a "secret" location, though it does contain one of the six Seals necessary to unlock Altaïr's Armor. In addition, the last secret location in the secret locations tab of the DNA menu is also an Assassin Tomb, but does not hold one of the Seals necessary to unlock Altaïr's Armor.

Templar Lairs
The Templar Lairs (with the exception of the Palazzo Medici) hide treasure that presumably belonged to and funded the activities of the Templar Order. All of these can be accessed through a wooden door, marked with a large red cross.
 * Palazzo Medici in Florence (GameStop pre-order exclusive for US versions, Master Assassin and Black Limited Editions, or by purchasing the Bonfire of the Vanities DLC).
 * Santa Maria Dei Frari in Venice (GameStop pre-order exclusive for US versions, Master Assassin, White and Black Limited Editions, or by purchasing the Bonfire of the Vanities DLC).
 * Arsenal Shipyard in Venice (included in Best Buy edition, Black Limited Edition, or by purchasing the Bonfire of the Vanities DLC).

Assassin's Creed: Brotherhood
Secret locations return in Assassin's Creed: Brotherhood, in the form of Lairs of Romulus. Like Assassin's Creed II, there are six of them, all spread throughout the vast city of Rome. Additionally, there are two Templar Lairs which may be obtained as a Pre-Order bonus, or with special editions of Brotherhood.

Completing all of the Lairs of the Followers of Romulus will allow Ezio to obtain two of the treasures they guard, the Armor of Brutus and the Dagger of Brutus. Through traversing these locations, Ezio will also obtain some special documents that give background of the cult.

Lairs of Romulus

 * Catacombe di Roma
 * Terme di Traiano
 * Il Colosseo
 * Cloaca Maxima
 * Palazzo Laterano
 * Basilica di San Pietro

Templar Lairs

 * Aqueducts
 * Trajan Market

Trivia

 * In the tomb hidden at Santa Maria Delle Visitazione, if you activate the lever, stand on the edge of the floor and stare into the water, you'll see a large figure move through the water after a minute, swimming past while staring at you with what appears to be a yellow eye. After the lever's time limit runs out, when you re-activate it and stand on the same spot and wait, a giant tentacle will shoot out of the water, though Ezio dodges before it manages to hit him.
 * Solomon's Temple in Assassin's Creed is considered to be similar to a secret location; or more precisely, a Templar Lair, due to its linear mission and being underground.
 * In the tomb in the Basilica di San Marco, the banners clearly show the poison symbol, despite the Seal bearing the snake symbol.