Perfluoroalkyl-containing compounds have a unique ‘fluorous’ property that refers to the remarkably specific affinity they share. Fluorous compounds can be easily isolated from non-fluorous species on the perfluoroalkyl-functionalized stationary phases used in fluorous solid-phase extraction and fluorous liquid chromatography by means of fluorous–fluorous interactions (fluorophilicity). Recently, this unique specificity has been applied to the highly selective enrichment and analysis of different classes of biogenic and related compounds in complex samples. Because the biogenic compounds are generally not ‘fluorous’, they must be derivatized with appropriate perfluoroalkyl group-containing reagent in order to utilize fluorous interaction. In this review, we introduce the application of fluorous affinity techniques including derivatization methods to biogenic sample analysis.