The toxicity of two types of ultra-small zeolites (8–18 nm) with LTL- and EMT-type structures is reported. Both the LTL- and EMT-type zeolites belong to the same group of molecular sieves; they have large pores (7.1–7.5 Å) and low silica content (Si/Al = 1.2–2.3). The zeolites are prepared by an environmentally friendly synthetic approach from precursor suspensions without using any organic template. Cellular interactions with the two types of zeolite nanocrystals are evaluated by cell viability, reactive oxygen species and cell life cycle assays. It is found that various concentrations of zeolites have negligible effects on the cell life cycle. Moreover, the LTL- and EMT-types zeolites did not cause extensive oxidative stress on the cells. Although it is seen that the zeolites extensively entered in the cells, there is no sign of toxicity for all employed concentrations of ultra-small EMT and LTL zeolites. Additionally, no abnormality in DNA replication while exposed to the zeolites is observed. Very importantly, the zeolite corona shows a high affinity for fibrinogen, moderate affinity for apoA-II and complement factor 3, and trace affinity for albumin, which is the most abundant protein of human plasma. Thus the zeolite nanoparticles can be considered as very promising material for purification of fibrinogen and lipoproteins. Since fibrinogen is considered as acute phase protein and found to be the most associated biomolecule in the composition of corona at the surface of zeolites, we propose that these nanoparticles can be potentially pro-inflammatory forin vivo applications.