The fusion and thermal decomposition of thirty-three diselenide compounds with a urea, thiourea or selenourea group linked with different aliphatic or aromatic substituents have been studied by thermogravimetry, differential scanning calorimetry and mass spectrometry in order to perform comparative thermal stability studies among analogs. A relationship has been found between stability and a series of effects which occur in the compound structures. Analysis of the thermal data indicated that: (a) in general, compounds with a urea or selenourea group are more stable than those with a thiourea group; (b) no difference in stability exists when an aromatic or aliphatic group is linked to the thiourea group but when linked to the urea or selenourea groups, stability does differ; (c) selenourea compounds with aliphatic chain are the most unstable; and (d) the nature of the substituent located on the benzyl ring has no effects on thermal stability. Therefore, criteria for the selection of substituents can be established in order to improve the stability of these drugs. In addition, the mass spectral fragmentation in comparison with thermal analytical data helps in confirming the thermal behavior of the compounds.