To feed 10 billion people in 30 years from now will heavily depend on new higher yielding, yet safe, biotech crop varieties. Biotech varieties are crops developed using biotechnologies, particularly genetic transformation and genome editing. A clean transgenic plant is a plant that contains only the defined foreign DNA fragment (transgene) in a defined genomic location, while a clean gene-edited plant is a plant free of any foreign DNA. Here we present the CTREP-finder, a user-friendly web server for fast detection, characterization and visualization of any foreign DNA fragment in TREPs, based on next-generation whole genome sequencing data. This server facilitates the rapid selection of clean transgenic or edited plants (CTREPs) for crop breeding programs, thus clear the biosafety concerns relating to plasmid backbone fragment insertions, with little requirement for bioinformatics expertise.