Perfluoroalkyl-containing compounds show a unique "fluorous" property, which is related to the specific affinity, i.e. fluorophilicity, between perfluoroalkyl groups. Therefore, fluorous compounds can be easily and selectively isolated from non-fluorous compounds utilizing liquid-liquid extraction, solid phase extraction, and liquid chromatographic techniques via their fluorophilicity. We have also developed novel methods for the selective analysis of biogenic-related compounds using fluorous separation techniques. These methods involve the attachment of perfluoroalkyl groups to target analytes, followed by their selective separation from endogenous biological matrices with appropriate fluorous separation techniques. Because the perfluoroalkylated compounds are generally not included in biological matrices, highly selective analysis of perfluoroalkyl-attached target analytes is possible. This review summarizes our recent works concerning biogenic-related compound analysis methods using fluorous separation techniques.