The molecular aggregation structure evolution during uniaxial stretching deformation and the uniaxial tensile mechanical properties for an environmentally benign and biodegradable segmented poly(urethane-urea) (SPUU) elastomer based on an alpha-amino acid lysine-based diisocyanate (LDI) was investigated. The performance was compared with a conventional SPUU elastomer consisting of a symmetric aliphatic short chain diisocyanate (1,4-butane diisocyanate). Both SPUUs contain a 1,4-butanediamine chain extender and poly(epsilon-caprolactone) soft segments. The evolution of molecular aggregation structure during stretching was monitored using in-situ simultaneous small-angle X-ray scattering and wide-angle X-ray diffraction. The LDI-based SPUU film contains weakly aggregated, disordered hard segment domains that readily dissociate upon mechanical deformation. The permanent deformation through fragmentation of the hard segment domains and strain-induced crystallization are associated with the low strength and large hysteresis loss of the LDI-based SPUU. (C) 2015 Published by Elsevier Ltd.