In a search for cold-regulated genes that are differentially expressed in alfalfa genotypes of contrasting freezing tolerance, we screened 1036 arrayed cDNA clones. The screening resulted in isolation of cDNA clones, which demonstrated dramatic differences in expression between hardy and un-hardy alfalfa varieties. Detailed analysis revealed that these cDNAs represent parts of novel non-coding repetitive elements carrying long-terminal repeats (LTR) and other retroelement-like features. Despite strong expression under low temperatures, DNA templates remained highly methylated, and a drug-induced decrease in methylation did not activate transcription under normal temperatures. We identified that these repetitive elements represent a large family and could insert into, or be adjacent to, the unrelated polyprotein sequences of putative retrotransposons. These retrotransposons also showed low temperature-induced transcriptional activation; however, this activation was not genotype-dependent. The retroelements described in this study are the first retroelement characterized in the Medicago genus. Furthermore, they represent the only known example of genotype-specific cold-induced transcriptional activation of multiple copies of a repetitive element whose expression is associated with a genotype difference in cold acclimation.