Compounds that have the same molecular formula, but are not identical are called isomers. There are two main classes of isomers, constitutional isomers and stereoisomers. Constitutional isomers will have the same number and types of atoms, but the sequence in which the atoms are connected is different (they have a different "constitution"). A simple example of constitutional isomers is ethanol and dimethyl ether, shown below.

In stereoisomers, the atoms are connected sequentially in the same way, such that condensed formulas for the two molecules are identical. The isomers differ, however, in the way the atoms are arranged in space. There are two major sub-classes of stereoisomers, conformational isomers, which interconvert through rotations around single bonds, and configurational isomers, which are not readily interconvertable.

Configurational isomers are, in turn, comprised of enantiomers and diastereomers. Enantiomers are stereoisomers which are related to each other as mirror images. Enantiomers can contain any number of stereogenic centers, as long as each center is the exact mirror image of the corresponding center in the other molecule.

If one or more of these centers differs in configuration, the two molecules are no longer mirror images, but are totally different chemical compounds with differing physical and biological properties. Stereoisomers which are not enantiomers are called diastereomers.

For a molecule with multiple chiral centers, the number of possible diastereomers is given by the equation:

where x is the number of possible isomers and n is the number of stereogenic centers. Thus, for molecules with two stereogenic centers there are four possible stereoisomers. For cholesterol, with eight stereogenic centers, there are 256 possible stereoisomers, etc.

A third type of stereoisomer which must be considered is a meso compound. A meso compound contains at least two stereogenic centers, yet the molecule itself is not chiral. This is because meso compounds contain an internal plane of symmetry; the molecule can be split by an imaginary mirror so that all atoms on one side of the mirror are the exact reflection of the atoms on the other side. This can be seen below for cis-1,2-dimethylcyclopentane; there are two chiral centers in the molecule since the two carbons labeled with the red asterisk are each bonded to four different groups. A mirror placed through the molecule, along the plane indicated by the dashed line, will exactly bisect the molecule with all groups exactly reflected by their counterparts on the other side of the "mirror".

Stereoisomers which are not chiral, and yet still have a different constitution, are another sub-class of diastereomers, the best known of which are simple cis - trans isomers, as shown below.

The relationship between isomers is summarized in the diagram given below.