The most precise, effective, and widely used tool for editing the genome is currently the clustered regularly interspaced short palindromic repeat (CRISPR), which represents the prokaryotes adaptive immune defense. The CRISPR/Cas-9 genome editing system relies on two key elements; mainly the guide RNA (gRNA) and CRISPR-associated (Cas-9) proteins. A complementary base pair in the designed sgRNA allows it to recognize the target sequence in the gene of interest. Either the non-homologous end joining or the homology-directed repair can be used to repair the double-stranded breaks, which are created by Cas-9 nuclease at a position upstream from a protospacer adjacent motif. The modified genome-editing tool CRISPR/Cas-9 has numerous applications in the various fields, such as biotechnology and medicine. Moreover, it is being studied for cancer management; Human Immunodeficiency virus (HIV), and as a gene therapy for several genetic diseases, including cystic fibrosis; sickle cell disease, and Duchenne muscular dystrophy. However, immunogenicity; off-target effect, and efficient delivery systems withstand against its spread in the clinical applications until introducing an improvement. The aim of this review was to summarize how the various CRISPR systems work; their important medical applications, and their limitations.