Vascular graft infection is still a life-threatening complication of reconstructive surgery. Among other options, application of cryopreserved homografts can eventuate favorable outcome, if graft replacement is necessary. The preparation and storage of these allografts need special infrastructure and deep subzero (− 80 °C) temperature. However, the longer storage time can lead to inferior results after implantation, based upon clinicians’ experiences. The goal of our investigation was to circumscribe the optimal storage time interval with differential scanning calorimetry (DSC) and histological evaluation, using porcine aorta. All samples were deep-freezed using − 80 °C. Cryopreservated grafts were melted after 4, 6, 12, 16, 20, 24, 28 and 52 weeks; then, DSC and different types of histology were performed. Light microscopy analysis showed significant changes in the connective tissue fibers’ structure from the 16th week; while, DSC measurements confirmed systematic decrease in the thermal stability from the same week during the follow-up period. Our investigation suggested that cryopreservation can lead to significant and increasing microstructural damage of the fibers following the 12th week; thus, the homograft implantation can result in higher success rate inside this timeframe.