"CRISPR" is an acronym of "Clustered, Regularly Interspaced, Short Palindromic Repeat". CRISPRs are regions of the genome containing short repeats (23 to 47 bp long) that are found in the genomes of many prokaryotes and Archaea.

Each CRISPR holds onto these short fragments of foreign DNA in order to function as a bacterial immune system: these short elements can be used to recognize and silence invading genetic material similarly to the RNA interference process in eukaryotes.

The figure below shows a genomic region containing a CRISPR. Red substrings correspond to CRISPR repeats, and blue substrings correspond to nonrepeating intervals called spacers. Repeats are highly palindromic, and their transcribed RNA forms a hairpin loop during RNA folding.