Cyclodextrins belong to cyclic oligosaccharides comprised of α-(1,4) linked glucopyranose groups. Their interesting supramolecular cavity-like structure can host active molecules providing a breeding ground for drug delivery systems. Cyclodextrins, due to their unique functional structure, can produce host-guest complexes with active ingredients, such as drugs, peptides, proteins, etc.; the complexes resulted from intramolecular interactions leading to stable molecules vehicles. Moreover, cyclodextrins are already applied in pharmaceutical industry applications since they can induce the solubility of lipophilic compounds and provide bioavailability and excellent safety profile and stability. In this review, the basic background for cyclodextrins and their current applications in the antimicrobial field are discussed. Besides, the antibacterial and antifungal-applications in the pharmaceutical field attract most researchers because of microbes' resistance. Regarding this, the most recent cyclodextrin inclusion complexes with antimicrobial and antifungal drugs are summarized in this article.