The aim of the study was the evaluation of selected species of meadow plants obtained from the first cut from the area covered by the agri-environmental program ‘Natura 2000’ in terms of the presence of cytotoxic compounds detected by the MTT test and the level of fungal contamination. The research was carried out on plant species that were evaluated differently in previously used methods for quality assessment of pasture feeds according to Klapp and Filipek. Twenty-six plant species were harvested in 2014 from meadows located in the valley of the Bydgoszcz Canal. Mycological examination of meadow plant samples was carried out according to PN-ISO 7954:1999. Cytotoxicity evaluation was performed using the MTT [3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] test. Selected samples were also subjected to evaluation of the endophytes occurrence in grasses using PCR. Natural meadow positions included in the study were dominated by moulds belonging to Humicola spp., Alternaria spp., Cladosporium spp., Torula spp., Fusarium spp. and Mucor spp. The highest level of fungal contamination was observed for Carex acutiformis Ehrh. The most infested grasses were Deschampsia caespitosa (L.) P.Beauv., Festuca arundinacea Schreb. and Lolium perenne L. The MTT test showed that the most cytotoxic species were Arrhenatherum elatius (L.) P.Beauv. (IC50 1.563 mg/mL) and Ranunculus repens L. (IC50 3.125 mg/mL). Epichloë endophytes were detected in one of 13 examined grass samples. Our own research suggests that previously used feed quality assessments should be verified by introducing modern methods of molecular biology and instrumental analysis. Results of this study may broaden the knowledge of the causes of problems resulting from feeding of roughage, mainly from natural meadows, and help in creating new rankings of the feed value of meadow sward components.