The genetic background of the immune response of rye to leaf rust (LR), although extensively studied, is still not well understood. The recent publication of the genome of rye line Lo7 and the development of efficient transcriptomic methods has aided the search for genes that confer resistance to this disease. In this study, we investigated the potential role of rye orthologs of wheatLrgenes (Lr1,Lr10,Lr21,Lr22a, andRGA2/T10rga2-1A)in the LR seedling-stage resistance of inbred rye lines D33, D39, and L318. Bioinformatics analysis uncovered numerousLrorthologs in the Lo7 genome, namely, 14ScLr1, 15ScRga2, and 2ScLr21paralogs, and 1 each ofScLr10andScLr22agenes. The paralogs ofScLr1,ScRga2, andScLr21were structurally different from one another and their wheat counterparts. According to an RNA sequencing analysis, only four wheatLrgene orthologs identified in the Lo7 genome (ScLr1_3,ScLr1_4,ScLr1_8, andScRga2_6) were differentially expressed; all four were downregulated after infection with compatible or incompatible isolates ofPuccinia reconditaf. sp.secalis(Prs). Using a more precise tool, RT-qPCR, we found that two genes were upregulated at 20 h post-infection, namely,ScLr1_4andScLr1_8in lines D33 and D39, respectively, both of which have been found to be resistant to LR under field conditions and after treatment with a semi-compatiblePrsstrain. We were unable to discern any universal pattern of gene expression afterPrsinfection; on the contrary, all detected relationships were plant genotype-,Prsisolate-, or time-specific. Nevertheless, at least someLrorthologs in rye (namely,ScLr1_3 ScLr1_4,ScLr1_8, andScRga2_6), even though mainly downregulated, may play an important role in the response of rye to LR.