The Cipher Lab, known as the Shadow Pokémon Lab or the Mystery Lab in Pokémon Colosseum, is a facility built by Cipher in the middle of the Orre desert. It was at this lab that Ein converted snagged Pokémon into Shadow Pokémon.

In Pokémon Colosseum, the newly-constructed laboratory has several levels and seven Cipher Peons, including Skrub guarding the lab from intruders. Several Researchers also populate the lab and will attempt to stop intruders from interfering. The elevators and security doors create a maze-like pathway. In addition, an alarm system is in place to alert seen intruders.

The only way to enter Ein's private laboratory is to enter the names of the three Pokémon whose DNA is hidden throughout the Shadow Pokémon Lab.

Beneath the laboratory is the end of the Under Subway. Colo 9

Later in the game, after Wes has defeated Evice and cleared Snagem Hideout out for the first time, the Cipher Peons that initially guarded the lab, besides Skrub return along with an additional one, who has a shadow starter who attempts to recover the data on how to create Shadow Pokémon. Wes again takes all of them down and the lab is seemingly abandoned. Colo 13

In Pokémon XD, Cipher Admin Lovrina has brought the Lab back into use after five years of dormancy. During this time, she and her team researches a way to make Shadow Pokémon impossible to purify. As the electric fence no longer works, the lab can be accessed from the main entrance. As such, the lab security seems to run backwards during this time: Ein's laboratory is one of the first rooms that Michael enters, as opposed to being one of the last. XD 4

The lab isn't well-concealed, and it can easily be seen from Agate Village and Mt. Battle.

250Ho-Oh 196Espeon 133Eevee 197Umbreon 249Lugia-Shadow
Phenac CityPyrite TownThe UnderAgate VillageGateon Port
Pokémon HQ LabKaminko's HousePyrite BuildingONBSPyrite CaveRelic CaveRelic StonePoké SpotsCipher LabThe Under SubwayS.S. LibraEclo CanyonSnagem HideoutCipher Key LairCitadark IsleOutskirt Stand
Phenac StadiumPre GymPyrite ColosseumUnder ColosseumRealgam ColosseumDeep ColosseumOrre Colosseum
Tournament areas
Mt. BattleRealgam Tower