The stability of Ngn@B12N12 and Ng n@B16N16 systems is assessed through a density functional study and ab initio simulation. Although they are found to be thermodynamically unstable with respect to the dissociation of individual Ng atoms and parent cages, ab initio simulation reveals that except Ne 2@B12N12 they are kinetically stable to retain their structures intact throughout the simulation time (500 fs) at 298 K. The Ne2@B12N12 cage dissociates and the Ne atoms get separated as the simulation proceeds at this temperature but at a lower temperature (77 K) it is also found to be kinetically stable. He-He unit undergoes translation, rotation and vibration inside the cavity of B 12N12 and B16N16 cages. Electron density analysis shows that the He-He interaction in He2@B 16N16 is of closed-shell type whereas for the same in He2@B12N12 there may have some degree of covalent character. In few cases, especially for the heavier Ng atoms, the Ng-N/B bonds are also found to have some degree of covalent character. But the Wiberg bond indices show zero bond order in He-He bond and very low bond order in cases of Ng-N/B bonds. The energy decomposition analysis further shows that the Eorb term contributes 40.9% and 37.3% towards the total attraction in the He2 dimers having the same distances as in He 2@B12N12 and He2@B 16N16, respectively. Therefore, confinement causes some type of orbital interaction between two He atoms, which akins to some degree of covalent character. © 2014 AIP Publishing LLC.