Grapevine is susceptible to many viruses and viroids that often have high economic impact. Until recently, their detection was based on traditional methods (ELISA, RT-PCR), which however do not allow the complete characterization of a plant sample’s virome. The last years this was made possible with the application of high-throughput sequencing (HTS), an holistic method that facilitates discovery of diverse and previously unknown viruses/viroids. With the aid of HTS, we attempted to elucidate the virome diversity of Greek vineyards, with an ultimate goal to unveil the etiology of unknown diseases, improve diagnostics and assist the production of high quality propagating material. For this purpose samples were selected, based on their geographic origin, variety, age and symptomatology. Total RNA (from single plants or pooled samples) was subjected to HTS. For the analysis of the obtained data, a grapevine optimized pipeline was developed, which produced large contigs for the majority of the viruses present in each sample. The analysis revealed the presence of many viruses reported for the first time in Greece, as well as a few contigs which may represent novel virus species. Interestingly, different genomic variants of Vitivirus species often co-existed in the same grapevine. The high number of viral populations identified, in the small number of grapevines tested, highlight the complex nature of the grapevine virome. Importantly, the obtained data on virus genetic diversity will help to improve diagnostics for the reliable virus indexing in grapevine certification schemes.