Though borrowing heavily from predecessors in the genre, the game added a new dymanic to gameplay, the ability to switch, at any time, between the various clones in order to complete puzzles that require more than one hand. Additionally, Clydes can combine their DNA with various animals in special machines that give them access to new abilities. Each Clyde may only be mutated once, but, upon completion of all levels under par time, the player may choose "Mutant Clyde" under the cheat menu and gain access to all abilities simultaneously, except for those of the Rock Transformation.

The Clydes must complete a series of 25 levels, accessible by entering various portals scattered across the lab, in order to be free. Like many platformers, the levels are often themed, taking on the appearance of swamps, the arctic, etc. Addtionally, there are 10 optional challenge levels that are not required to beat the game (but must be completed to attain all 12 achievements).

Only one Clyde may exit the portal in each level, however, there are a number of air vents into which the excess Clyde clones can escape. Though not required to complete the level, completion of this task offers bonus points and the chance to earn an achievement.

There are also a number of "Killer Kenn" action figures that were also cloned and can be collected for bonus points. Two achievements are also tied into the collection of these figures.

Xbox Live

Cloning Clyde offers two online modes of play to subscribers of Xbox Live's Gold service, Co-Op and Versus. Co-Op features the original levels of the game, but allows multiple players, each controlling a Clyde, to work together. Versus, on the other hand, features two teams of Clydes, each responsible for defending a set of security machines from their opponents. The first team to destroy all of its opponents' machines wins.