Flavonoids are a large class of naturally occurring aromatic secondary plant metabolites. They constitute one of the most characteristic classes found in nature and more than 4000 flavonoids have been identified and divided into several subclasses. Flavonoids have several effects on human health, mainly related to their antioxidant activity. As a result of the increased interest in the biologically active compounds in food, many research studies have investigated the detection and quantification of antioxidants. Citrus plants are of great interest since they accumulate large amounts of flavonoids and fruit and juices of these species are consumed in large quantities. Despite the extensive research performed on Citrus flavonoids, many compounds still remain unidentified. In this work, flavonoids of five citrus juices: lemon, grapefruit, bergamot, orange, and mandarin were analyzed by microHPLC coupled on-line with an MS detector equipped with an ESI source operating in negative mode. The use of microcolumn HPLC greatly enhanced detection performance. In total, 20 flavonoids of two different subclasses (flavanone and flavone glycosides) were identified with the help of retention data and MS spectral information.