The clustered regularly interspaced short palindromic repeats (CRISPR) and associated proteins (CRISPR-Cas) systems are the hot research topics recently. In addition to their important roles in gene editing, CRISPR-Cas has a good prospect in the diagnosis of infectious diseases. Traditional diagnostic techniques for infectious diseases and molecular detection are inadequate in terms of operation, detection cycle, sensitivity and specificity. With the in-depth study of the CRISPR-Cas systems, the application of detection technology for infectious pathogens can be carried out in view of its specific nucleic acid recognition and genetic modification functions. At present, Cas9, Cas12a and Cas13 nucleases have been found to be the main ones that can be used for detection. The technology with high efficiency, specificity and programmability can be used for the detection of Zika virus, dengue, malaria, mycobacterium tuberculosis, human papilloma virus, Ebola, hepatitis B virus and severe acute respiratory syndrome corona virus 2, and a series of infectious diseases pathogens, which could become a rapid, sensitive, specific, cheap and reliable diagnosis technology, and provide important theoretical basis for the diagnosis of infectious diseases. This paper mainly reviews the application and progress of Cas9, Cas12a and Cas13 in the diagnosis of infectious diseases.