Thiolated polyaspartamides either with N,N-dimethyl-2-aminoethyl (DME), N,N-dimethyl-3-aminopropyl (DMP) or 2-hydroxyethyl (HE) side groups were synthesized to study the effect of side groups on the hydrolytic stability of these polymers. The chemical structure of linear polymers was confirmed by 1H NMR spectroscopy, while thiol content was determined by Ellman's assay. Hydrolytic stability of thiolated polyaspartamides was studied by viscosity measurements and results suggested main-chain degradation in the presence of DME side groups. Polyaspartamides with DMP or HE side groups showed considerable stability. Thiolated polyaspartamides were converted to their disulfide cross-linked hydrogels and the gelation process was followed by oscillatory rheology. Time-dependence of dynamic moduli indicated the degradation of hydrogels containing DME side groups, while stable moduli were observed for hydrogels containing DMP or HE side groups. This structure-dependent aqueous degradation of polyaspartamides can be useful in different biomedical fields.