Molecularly imprinted polymers (MIPs) are a type of artificial polymer, which have complementary cavities that are designed to bind a specific target molecule with a high degree of selectivity. Due to their effectiveness and stability, MIPs have found their way into many applications in medicine, chemistry, analysis and sensing fields. One of the most important modern uses of MIPs is the recognition of biological molecules of medical significance, which are called “biomarkers”. The use of MIPs enables easy and rapid extraction and detection of these biomarkers from different biological matrices. There are multiple techniques that arose for synthesis of MIPs each with their own set of advantages and drawbacks. In this review, we discuss MIPs in detail including their different types, methods of synthesis, characterisation methods, common challenges, in addition to their applications in different fields with a focus on their use in the analysis of protein biomarkers.