This article focuses on the occurrence of Fusarium species on barley kernels in Slovakia. The study was conducted over two consecutive crop years (2004–2005) on three cultivars (potential malting varieties) at five locations in Slovakia. Fusarium spp. were detected in all locations and years ranging from 0.1 to 27% seed infestation. The highest infestation of kernels was recorded in 2005 for all localities and all cultivars. The following species were detected: Fusarium acuminatum, F. arthrosporioides, F. avenaceum, F. culmorum, F. chlamydosporum, F. equiseti, F. graminearum, F. langsethiae, F. nivale (syn. Microdochium nivale), F. oxysporum, F. poae, F. sambucinum, F. semitectum, F. solani, F. sporotrichioides, and F. tricinctum. The most common was F. poae in all localities and cultivars, with an isolation frequency ranging from 0.33 to 11.67%. This is the first report of F. langsethiae occurrence in Slovakia with an isolation frequency ranging from 0.33 to 6.67%. In 2005 a wider spectrum of Fusarium species, a higher level of kernel infestation, and a lower germinative activity was recorded than in 2004. The germinative activity of kernels was impaired the most in 2005 irrespective of cultivar. The decreasing of germinative activity in 2005 corresponded with higher kernel infestation with Fusarium fungi.