The size-dependent elastic behavior of silicon nanocantilevers and nanowires, specifically the effective Young’s modulus, has been determined by experimental measurements and theoretical investigations. The size dependence becomes more significant as the devices scale down from micro- to nano-dimensions, which has mainly been attributed to surface effects. However, discrepancies between experimental measurements and computational investigations show that there could be other influences besides surface effects. In this paper, we try to determine to what extent the surface effects, such as surface stress, surface elasticity, surface contamination and native oxide layers, influence the effective Young’s modulus of silicon nanocantilevers. For this purpose, silicon cantilevers were fabricated in the top device layer of silicon on insulator (SOI) wafers, which were thinned down to 14 nm. The effective Young’s modulus was extracted with the electrostatic pull-in instability method, recently developed by the authors (H Sadeghian et al 2009 Appl. Phys. Lett. 94 221903). In this work, the drop in the effective Young’s modulus was measured to be significant at around 150 nm thick cantilevers. The comparison between theoretical models and experimental measurements demonstrates that, although the surface effects influence the effective Young’s modulus of silicon to some extent, they alone are insufficient to explain why the effective Young’s modulus decreases prematurely. It was observed that the fabrication-induced defects abruptly increased when the device layer was thinned to below 100 nm. These defects became visible as pinholes during HF-etching. It is speculated that they could be the origin of the reduced effective Young’s modulus experimentally observed in ultra-thin silicon cantilevers.