The stability of polyurethane (PU) is of critical importance for applications such as in coating industry or as biomaterials. To eliminate the environmental concerns on the synthesis of PU which involves the use of organic solvents, the aqueous-based or waterborne PU (WBPU) has been developed. WBPU, however, may be unstable in an electrolyte-rich environment. In this study, the authors reported the stability of biodegradable WBPU in the buffered saline solutions evaluated by atomic force microscopy (AFM). Various biodegradable WBPU films were prepared by spin coating on coverslip glass, with a thickness of ∼300 nm. The surface AFM images of poly(ε-caprolactone) (PCL) diol-based WBPU revealed nanoglobular structure. The same feature was observed when 20% molar of the PCL diol soft segment was replaced by polyethylene butylenes adipate diol. After hydration in buffered saline solutions for 24 h, the surface domains generally increased in sizes and became irregular in shape. On the other hand, when the soft segment was replaced by 20% poly(l-lactide) diol, a meshlike surface structure was demonstrated by AFM. When the latter WBPU was hydrated, the surface domains appeared to be disconnected. Results from the attenuated total reflectance infrared spectroscopy and x-ray photoelectron spectroscopy indicated that the surface chemistry of WBPU films was altered after hydration. These changes were probably associated with the neutralization of carboxylate by ions in the saline solutions, resulting in the rearrangements of soft and hard segments and causing instability of the WBPU.