The origin and initial purpose of the Flesh Pits have never been truly explained, and is thus subject to speculation. It is known, however, that they were used to create creatures, likely to do Shang Tsung's and Shao Kahn's bidding.
The only known characters who emerged from the pits and fought in Mortal Kombat were Meat (who was originally a secret skin in Mortal Kombat 4 and was then later transformed into an official character in Mortal Kombat: Armageddon), Mileena (confirmed in the second portion of her biography concerning the 2011 Mortal Kombat video game), and Skarlet (an enforcer of Shao Kahn created by mixing warrior blood and sorcery). Another creation was the Flesh Pits Mutant, one of Shang Tsung's failed Flesh Pits experiments which guarded the souls in the Krypt.
After Shang Tsung's demise, the Flesh Pits on his private island were used by the Cleric of Chaos, Havik, as part of his twisted rituals involving the corrupted Blood Magik linked to the Kamidogu daggers he was seeking to collect. Havik also used the Flesh Pits to revive a recently killed Reiko in conjunction with the Blood Code empowering the Outworld General.
In Mortal Kombat 11, Kotal Kahn reveals to a time displaced Jade that Shao Kahn betrayed him and had him captured to be tortured and experimented on in Shang Tsung's Flesh Pits, the sorcerer's death sometime later allowing him to escape to freedom.
- While the Flesh Pits were originally believed to be in Outworld, near Shao Kahn's imperial palace, the Mortal Kombat X (Comic Series) has shown them to be located on Shang Tsung's Island. It has not been confirmed if these are the same Flesh Pits seen in Mortal Kombat (2011 video game) or if more than one laboratory exists.