Until today there is no publicly available bioinformatics tool for plant virus discovery. We have developed an online package, VirFind, with the purpose to facilitate virologists with virus detection and discovery using next generation sequencing. This is an automated bioinformatics pipeline that can accept input files in 454, Illumina or fasta formats, and filter out host reads, virus reads with their corresponding Blastn and Blastx reports, and perform conserved domain search for reads of unknown origin. Using VirFind to process over 30 plant samples sequenced with 454 or Illumina platforms, we have detected various viruses and extended genome sequences of Elderberry latent virus (<i>Carmovirus</i>, <i>Tombusviridae</i>) in elderberry, Mint vein banding-associated virus (unassigned genus, <i>Closteroviridae</i>) in mint, and <i>Peach rosette mosaic virus</i> (<i>Nepovirus</i>, <i>Secoviridae</i>) in grape. We also discovered seven novel virus species including a trichovirus and a waikavirus in blackcurrant, and five carlaviruses in elderberry. Furthermore, VirFind was independently and successfully tested by four external users with seven different dsRNA, siRNA or total RNA datasets from plants or insects, demonstrating that the tool can be used as a universal virus discovery package. VirFind is now open on the internet with a front-end graphical interface for public use.