The secret caves (also formatted as Secret Cave and alternatively named Crystal Caves or Banana Bird caves) are a series of caverns that contain an imprisoned Banana Bird and appear throughout the Northern Kremisphere. They only appear in Donkey Kong Country 3: Dixie Kong's Double Trouble!.
During Baron K. Roolenstein's invasion of the Northern Kremisphere, he trapped the Banana Queen behind an evil barrier and imprisoned every Banana Bird in a secret cave, to ensure that he would not be opposed. Throughout their adventure, Dixie and Kiddy Kong must rescue the Banana Birds trapped in every secret cave, one of which appears in every world, and a few on the Northern Kremisphere map itself. A few of the secret caves can only be reached with the help of a Brothers Bear, or by using the Gyrocopter.
When visiting a secret cave (which Cranky Kong introduces to the Kongs upon first visiting one in the Game Boy Advance port), the Kongs must participate in a concentration challenge and notice the sequence in which the red, green, yellow, and blue crystals flash in. Each crystal is arranged and colored the same as the , , , and buttons on a Japanese and European Super Nintendo Entertainment System controller, and each button causes its corresponding crystal to light up. The sequence in which the crystals flash is always random, and the player can replicate the sequence by pushing the buttons in the same order that the crystals flash in. In the Game Boy Advance port, the is used to activate the crystals; similarly, the crystals are activated based on which arrow button the player presses. A secret cave has a mostly empty scenery except for some tunnels that appear in the background.
By successfully replicating the order, the Banana Bird breaks out from the small crystal it is imprisoned in, and the Kongs obtain it. If the Kongs do not replicate the order correctly, they leave the secret cave and must re-enter it if they want to retry the challenge.