Demand is growing in the field of medical diagnostics for simple, disposable devices that also demonstrate fast response times, are easy to handle, are cost-efficient, and are suitable for mass production. Polymer-based microfluidic devices meet the requirements of cost efficiency and mass production and they are suitable for biosensor applications. Conducting polymer-based electrochemical sensors have shown numerous advantages in a number of areas related to human health, such as the diagnosis of infectious diseases, genetic mutations, drug discovery, forensics and food technology, due to their simplicity and high sensitivity. One of the most promising group of conductive polymers is poly(3,4-ethylenedioxythiophene) (PEDOT) and its derivatives due to their attractive properties: high stability, high conductivity (up to 400–600 S/cm) and high transparency. This review paper summarizes newly developed methods associated with the application of PEDOT to diagnostic sensing.