The threat of emerging infectious viruses in humans requires a more effective approach regarding virus surveillance. A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens and may lead to the identification of newly emerging pathogens in the future. In this study, diarrhoea samples from an outbreak of gastrointestinal illness in a Danish population of European roe deer were gathered for which no aetiological agent could be identified. Large-scale molecular RNA virus screening, based on host nucleic acid depletion, sequence-independent amplification and sequencing of partially purified viral RNA, revealed the presence of novel astroviruses, CcAstV-1 and CcAstV-2, in two of ten diarrhoea samples. Whether these viruses were responsible for causing diarrhoea remains to be determined. Phylogenetic analyses on amplified sequences showed that these viruses were most closely related to each other, were a novel species in the genus Mamastrovirus and may represent two different serotypes.