Viruses and viroids pose a significant threat to horticultural crops worldwide, leading to major economic losses thereby endangering food security. Thus, producing disease-free plant material is also crucial for the safe international exchange of germplasm. Shoot tip cryotherapy, based on the principle of cryopreservation has proven to be a promising approach that involves briefly exposing the excised shoot tips to liquid nitrogen. Following this eradication mechanism, it becomes crucial to screen the pathogen-free regenerants with the help of various confirmatory tests before releasing them into the field. In addition, detailed histological analyses of shoot tips post-cryopreservation and the distribution patterns of viruses and viroids using immunolocalization techniques have offered insights into the mechanism behind cryotherapy. The efficacy of various serological and molecular detection techniques has also been discussed to assess the phytosanitary status of plants after cryotherapy. Overall, this chapter provides up-to-date and extensive information on the effectiveness of shoot-tip cryotherapy for eliminating viruses and viroids from horticultural crops.