Extraction of endogenous compounds and drugs and their corresponding metabolites from complex matrices, such as biofluids and solid tissues, requires adequate analytical approach facilitating qualitative and quantitative analysis. To this end, solid‐phase microextraction has been introduced as modern technology that is capable of efficient and high‐throughput extraction of compounds due to its ability to amalgamate sampling, extraction, and pre‐concentration steps, while requiring minimal use of organic solvents. The ability of solid‐phase microextraction to enable analyses on small‐volume biological samples and growing availability of biocompatible solid‐phase microextraction coatings make it a highly useful technology for variety of applications. For example, solid‐phase microextraction is particularly useful for identifying biomarkers in metabolomics studies, and it can be successfully applied in pharmaceutical and toxicological studies requiring the fast and sensitive determination of drug levels, especially those that are present at low levels in biological matrices such as plasma, urine, saliva, and hair. Moreover, solid‐phase microextraction can be directly applied in in vivo studies because this extraction technique is non‐exhaustive and its biocompatible probes offer minimal invasiveness to the analyzed system. In this article, we review recent progress in well‐established solid‐phase microextraction technique for in vitro and in vivo analyses of various metabolites and drugs in clinical, pharmaceutical, and toxicological applications.