Cold storage of pomegranates is essential for prolonging postharvest storage and for the implementation of cold-quarantine insect disinfestation treatments required for international trading. However, pomegranates are chilling sensitive; they may develop chilling injuries upon exposure to unfavorable low temperatures. In this mini-review, we summarize molecular data obtained from three different RNA Seq transcriptome analyses of responses of pomegranate fruits to cold storage. These experiments included comparisons among the transcriptomic responses following a 2-week exposure to 1 °C in three different model systems: 1) unconditioned chilling-sensitive fruits versus relatively chilling-tolerant low-temperature-conditioned fruits; 2) chilling-sensitive early harvested fruits versus relatively chilling-tolerant late-harvested ones; and 3) chilling-sensitive ‘Ganesh’ variety versus the relatively chilling-tolerant ‘Wonderful’ variety. Comparisons among differentially expressed transcripts that were exclusively and significantly up-regulated in the relatively chilling-tolerant fruits in all three model systems enabled identification of 573 common chilling tolerance-associated genes in pomegranates. Functional categorization and classification of the differentially expressed transcripts revealed several regulatory, metabolic, and stress-adaptation pathways that were uniquely activated in response to cold storage in relatively chilling-tolerant fruits. More specifically, we identified common up-regulation of transcripts involved in activation of jasmonic acid and ethylene hormone biosynthesis and signaling, stress-related transcription factors, calcium and MAPK signaling, starch degradation and galactinol and raffinose biosynthesis, phenol biosynthesis, lipid metabolism, and heat-shock proteins. We hypothesized these pathways to be involved in imparting chilling tolerance to pomegranate fruits. © 2019 Society of Chemical Industry. © 2019 Society of Chemical Industry