Poly-l-lactide-co-ε-caprolactone (PLCL) is a unique polymer containing both polylactic acid and poly-ε-caprolactone (PCL) chain units, and thus it has better flexible and biodegradable properties. Based on these unique properties of PLCL, we have developed balloons that are now widely used in treating major medical problems [Biomaterials2016,105, 109–116]. One of the most important considerations needed for balloons is to ensure that the material properties remain similar after undergoing ethylene oxide (EtO) or gamma (γ-) sterilization treatments. From the biotechnological point of view, we focused on analyzing the vital molecular properties of the PLCL material after sterilization, such as changes in crystallinity, molecular weight distributions (Mw, Mn, and polydispersity index), and inherent viscosity (η). Analysis of the data reveals that EtO sterilization does not engender any change in crystallinity, melting temperature (Tm), molecular weights, and η of the polymer. On the contrary, γ-radiations induce chain scission and consequential decrease of ∼33 and ∼15% in molecular weights and η values, respectively. Based on our observations, we recommend EtO sterilization instead of γ-radiation for PLCL. This ensures prolonged stability of the polymer against degradation in a biological environment, long-shelf life, and absolute assurance that balloon failures do not occur after implantation.