Polymeric nanoparticles (NPs) derived from self-assemblies of amphiphilic polymers have demonstrated great potential in clinical applications. However, there are challenges ahead. Notably, immunotoxicity remains a major roadblock that deters the NPs from further applications. Studies suggested that the hydrophobic component is a primary cause, yet biocompatible hydrophobic carbohydrate-based polymers may help mitigate this issue. Herein we design and synthesize novel NP systems having glucose poly(orthoesters) hydrophobic scaffold and polyethylene glycol (PEG) hydrophilic shell. The new NPs exhibited low immunotoxicity both in vitro and in vivo, as measured by the induced cytokine levels. In contrast, when other polymers, such as polylactide (PLA) or polycaprolactone (PCL), were used as the hydrophobic scaffold, the cytokine levels were orders of magnitude higher. Results from our multiple immunological studies indicate that carbohydrate-based polymers can largely mitigate the hydrophobicity-induced immunotoxicity, and thereby they may be good candidate polymers to engineer low immunotoxic biomaterials for various biomedical studies.