In this research, gelatin nanoparticles were synthesized via inverse miniemulsion method by employing a mixture of a water soluble carbodiimide (CDI) and N-hydroxysuccinimide (NHS) as a non-toxic cross-linking system. The gelatin nanoparticles were characterized for their size and size distribution, morphology and stability and were compared with those of nanoparticles cross-linked by glutaraldehyde (GA) as the most commonly utilized cross-linking agent. The results showed the formation of more homogeneous nanoparticles with smaller size when CDI/NHS used as cross-linking agent under the same synthesis condition. Moreover, dilute solution viscosimetry experiments confirmed the stability of the nanoparticles under various physicochemical conditions. The differences in the characteristics of CDI/NHS and GA cross-linked nanoparticles were ascribed to the different nature of network formation using the two cross-linking agents. Generally, these results suggested CDI/NHS cross-linked gelatin nanoprticles as an interesting candidate for drug delivery application.