Different isotopes of the same element can be considered as different kinds of atoms when enumerating isomers of a molecule or ion. The replacement of one or more atoms by their isotopes can create multiple structural isomers and/or stereoisomers from a single isomer.
For example, replacing two atoms of common hydrogen () by deuterium (, or ) on an ethane molecule yields two distinct structural isomers, depending on whether the substitutions are both on the same carbon (1,1-dideuteroethane, ) or one on each carbon (1,2-dideuteroethane, ); as if the substituent was chlorine instead of deuterium.  The two molecules do not interconvert easily and have different properties, such as their microwave spectrum.
Another example would be substituting one atom of deuterium for one of the hydrogens in chlorofluoromethane ().  While the original molecule is not chiral and has a single isomer, the substitution creates a pair of chiral enantiomers of , which could be distinguished (at least in theory) by their optical activity.
When two isomers would be identical if all isotopes of each element were replaced by a single isotope, they are described as isotopomers or isotopic isomers. In the above two examples if all  were replaced by , the two dideuteroethanes would both become ethane and the two deuterochlorofluoromethanes would both become .
The concept of isotopomers is different from isotopologs or isotopic homologs, which differ in their isotopic composition. For example,  and  are isotopologues and not isotopomers, and are therefore not isomers of each other.