Glass disease is caused by an inherent fault in the chemical composition of the original glass formula. 
Glass contains three types of components: network formers  establish basic structure, network stabilizers make glass strong and water resistant, and flux lowers the melting point at which the glass can be formed.
Common formulations of glass may include silica (SiO) as a former, alkali oxides such as soda (NaO) or potash (KO) for flux, and alkaline earth oxides such as lime (CaO) for stabilizing.
Structurally, glass is composed of a network of SiO-tetrahedrons. In addition to the network former silicon which establishes its principal structure, glass contains network modifying agents such as the alkali ions Na+ and K+ and the alkali earth ions Ca+ and Mg+.  Glass does not have a defined stoichiometry, rather the network is flexible. It can incorporate other ions, depending upon factors such as the main composition and firing conditions of the glass. This causes almost all glass to be chemically unstable to some extent.
Electron charge differences of ions within the structure form the basis of its bonding. Both viscosity and transition temperature are related to the availability of oxygen bonds in the glass's composition.  Modifying agents tend to lower the melting point of the silica.   Higher contents of SiO increase acidity of the glass. Higher contents of CaO, NaO, and KO increase basicity.
The chemical stability of glass decreases when only NaO and KO are added as flux, because bonding becomes weaker. The chemical stability of glass can be increased by adding CaO, MgO, ZnO, and AlO. To be stable, glass composition must balance temperature lowering agents with stabilizing agents.
Exposure of a glass surface to moisture, either in solution or from humidity in the atmosphere, causes chemical reactions to occur on and below the surface of the glass. The exchange of alkali metal ions (from within the glass) and hydrogen ions (from outside) can cause chemical and structural changes to the glass. When alkali metal cations in the near-surface layer are replaced by smaller hydrogen ions, structural differences between the affected surface layer and the unaffected lower layers of glass cause increasing tensile stress, which in turn can cause cracking.
The likelihood of degradation due to glass disease depends on the amount and proportion of alkaline compounds mixed with silica, and on surrounding conditions.
Inadequate calcium oxide causes the alkalis in the glass to remain water-soluble at a low level of humidity. Exposure to higher levels of relative humidity during storage or display causes alkali to hydrate and leach out of the glass. Repeated changes in humidity can be particularly damaging. It is important to realize that any glass object can deteriorate if it is exposed to unsuitable environmental conditions. Crystal, historic glass, or treasured family items should never be exposed to the high temperatures and water pressure of a dishwasher.
Energy dispersive x-ray analysis (EDXA), scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS) can be used to study exchange reactions in different types of glass. By quantifying and studying chemical structure and reactions at the near-surface layer, the mechanisms of glass disease can be better understood. 
Measurement of the pH of glass surfaces is particularly important if glass objects have a matte surface, or have been exposed to kaolin or other substances. In the case of extremely small objects such as glass beads, pH measurement may be necessary to determine whether alkaline salts are present and changes in the glass are occurring.