CRISPR (“Clustered, Regularly Interspaced Short Palindromic Repeats”) sequences were found in almost all archaea and partially in bacteria and over past 20 years their role and possible applications have been studied. Protein Cas9, that is connected with those sequences, is a nuclease that, guided by short RNA molecule (guide RNA, gRNA) binds to the target DNA molecule and cleaves it. Transferability of Cas9 between the species has allowed multiple applications of CRISPR-Cas9 system in genetic engineering. Programmability of CRISPR-Cas9 system includes designing gRNA and choosing the repair pathway for induced double-strand break on DNA, but there are also possibilities like introducing mutations in Cas9 domains in order to influence system specificity. Development of techniques such as atomic force microscopy (AFM) will play a key role in visualization of CRISPRCas9 system in real-time. So far, plenty of fruit crops have been modified using CRISPR-Cas9 technology, but there has also been a lot of research of technology’s efficiency in field of human diseases. Perfecting the CRISPR-Cas9 technique is key for conduction of clinical trials, which will be of great importance in treatment of a wide spectrum of human diseases.