The results of studying the resistance of samples of naked oats from the world collection of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources and varieties of local breeding work to stem rust lesion are presented. The study was carried out in 20172019 in a field experiment in natural conditions in Kemerovo region. The influence of meteorological factors during the vegetation period of naked oat plants on the degree of disease damage was noted: more intense lesion was observed in years with low air temperatures and excessive moisture supply during the period of seedling-ear formation and a large amount of precipitation during the period of filling and maturation of grain. The results of phytopathological analysis of 50 collection samples of naked oats revealed that mid-late samples are more affected by stem rust (74.9% on average for the group). The study (n = 50) revealed the effect of stem rust lesion on the resistance to lodging of crops (r = –0.5751 at R = 0.273), grain size (r = –0.7737 at R = 0.273), and yield of naked oat samples (r = –0.9387 at R = 0.273). Naked oats are highly susceptible to pathogen lesion, 84% of the samples showed very low resistance with a damage index of more than 65.1%. Samples with a low damage degree were identified, characterized by high yield rates, 1000 grain weight, resistance to lodging and smut fungi, and a low level of segregation of hulled grains: Pennline 9010 (USA), Numbat (Australia), Progress (Omsk region), Gehl (Canada), Piband (Leningrad region), g/o-327-1/16, g/o-441-1/17, g/o-444-7/17 (Kemerovo region).