The article compares the relative stability of MCM-41 and related mesoporous materials in electron beam at an accelerating voltage of 100–300 kV. The work encountered in electron microscopy presents a comparison with similar research that has been carried out on nonporous and microporous silicates, especially α-quartz and zeolite Y. The trends in stability are analyzed, classifying the effects of sample preparation, organic and inorganic moieties, and electron accelerating voltage on beam stability. A higher synthesis temperature, the use of an acid catalyst in the synthesis, and the presence of additional organic or inorganic material within the channels were all found to stabilize these materials. The dose required to completely disrupt the structure increased with accelerating voltage for nearly all samples, suggesting a primarily radiolytic damage mechanism. The exception, MCM-41 containing nanometer-sized titania particles in its channels, was found to be almost insensitive to accelerating voltage.