Cytochrome P450 (CYP) is a superfamily of enzymes that plays a key role in the metabolism of drugs and numerous xenobiotics by introducing hydrophilic groups into their molecular structures. The major CYP enzymes involved in drug metabolism are CYP3A4, CYP2D6, CYP2C9, CYP1A2, and CYP2C19. Genetically determined differences or modulation of cytochrome P450 enzyme activity can lead to a variety of effects, including adverse drug reactions or loss of therapeutic effects. This paper provides an overview and comparison of the most commonly used methods for assessing the metabolic activity of cytochrome P450 enzymes. The general work flow of these methods is described, as well as the advantages and limitations of each method. These methods include high performance liquid chromatography (HPLC)-based methods, which are most often coupled with mass spectrometry (MS); fluorescence-based; luminescence-based; and radioactivity-based methods. Various studies where these methods have been applied for in vitro and in vivo evaluation of cytochrome P450 metabolic activity using specific markers are presented in this paper. Numerous activity measurements have been performed: for the purpose of phenotyping cytochrome P450 enzymes to optimize therapeutic outcomes; to determine the relationship between phenotype and genotype; for screening of modulatory effects of drug candidates and studying the inhibitory or inductive effects of drugs, herbs, food ingredients and additives; and also for comparisons of existing approaches and validation of new approaches for cytochrome P450 activity assessment.