Background Plants produce a wide variety of molecules, and some of them are of medicinal importance. Biotechnological systems such as suspended cells and hairy roots (HR) are used to produce plant compounds in a stable and controlled manner. HRs are obtained through a genetic transformation mediated by Rhizobium rhizogenes (R. rhizogenes), a Gram-negative bacterium that randomly inserts the transfer DNA (T-DNA) from the root-inducing plasmid (pRI) into the chromosome of a plant cell. Gene expression of T-DNA in plant cells induces a metabolic change to promote HR syndrome. The primary benefits of producing medicinal plant compounds in these biotechnology systems include the large yield of organ-specific bioactive compounds, production of de novo secondary metabolites, and scaling up to bioreactors for the industrial production of medicinal plant compounds. This article aims to describe the applications and advantages of the biotechnological system of hairy root cultures, which is used to obtain specific or de novo compounds of plant secondary metabolism in the last fourteen years. Methodology A broad bibliographic search was accomplished of articles that report the HR cultures to produce bioactive compounds of medicinal plants. To find the largest number of reports in the past fourteen years, different databases for web searchers, such as Scopus, PubMed, Google Scholar, Web of Science, Redalyc, and SciELO were used. The reports mentioned here were collected and selected to include those that were of great relevance. Results One hundred and twelve research articles were selected to integrate this review. We highlight the principal advantages of hairy root cultures to produce secondary metabolites which are used as medicinal compounds. Hairy root cultures can produce a wide variety of organo-specific compounds, including de novo secondary metabolites, by activating complex metabolic pathways. This process is facilitated by the expression of rol genes which are inserted into the chromosome of the plant cell during genetic transformation mediated by R. rhizogenes. Therefore, stable and continuous molecules production over several years, as well as a higher yield than that in wild plants, have been observed. Another advantage is the easy scaling up into a bioreactor system. Conclusions Different plant species have successfully produced HR. The root cells in HR cultures have a complicated endomembrane system that facilitates the production of a wide variety of bioactive molecules of the secondary metabolism, such as phenols, terpenes, and alkaloids. Due to the random insertion of the pRI rol genes, different secondary metabolism pathways are activated in each induced HR. Only a few HR lines synthesize higher concentrations of specific molecules found in the wild plant or de novo metabolites, including those used as medicinal compounds; and some of them are secreted into the culture medium.