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The long-term durability of cement-based materials is influenced by the pore structure and associated permeability at the sub-micrometre length scale. With the emergence of new types of sustainable cements in recent decades, there is a pressing need to be able to predict the durability of these new materials, and therefore nondestructive experimental techniques capable of characterizing the evolution of the pore structure are increasingly crucial for investigating cement durability. Here, small-angle neutron scattering is used to analyze the evolution of the pore structure in alkali-activated materials over the initial 24 h of reaction in order to assess the characteristic pore sizes that emerge during these short time scales. By using a unified fitting approach for data modeling, information on the pore size and surface roughness is obtained for a variety of precursor chemistries and morphologies (metakaolin- and slag-based pastes). Furthermore, the impact of activator chemistry is elucidated via the analysis of pastes synthesized using hydroxide- and silicate-based activators. It is found that the main aspect influencing the size of pores that are accessible using small-angle neutron scattering analysis (approximately 10–500 Å in diameter) is the availability of free silica in the activating solution, which leads to a more refined pore structure with smaller average pore size. Moreover, as the reaction progresses the gel pores visible using this scattering technique are seen to increase in size.