An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, 5'---TTACGnnnnnnCGTAA---3' is an inverted repeat sequence. When the intervening length is zero, the composite sequence is a palindromic sequence.

Both inverted repeats and direct repeats constitute types of nucleotide sequences that occur repetitively. These repeated DNA sequences often range from a pair of nucleotides to a whole gene, while the proximity of the repeat sequences varies between widely dispersed and simple tandem arrays. The short tandem repeat sequences may exist as just a few copies in a small region to thousands of copies dispersed all over the genome of most eukaryotes. Repeat sequences with about 10–100 base pairs are known as minisatellites, while shorter repeat sequences having mostly 2–4 base pairs are known as microsatellites. The most common repeats include the dinucleotide repeats, which have the bases AC on one DNA strand, and GT on the complementary strand. Some elements of the genome with unique sequences function as exons, introns and regulatory DNA. Though the most familiar loci of the repetitive sequences are the centromere and the telomere, a large portion of the repeated sequences in the genome are found among the noncoding DNA.

Inverted repeats have a number of important biological functions. They define the boundaries in transposons and indicate regions capable of self-complementary base pairing (regions within a single sequence which can base pair with each other). These properties play an important role in genome instability and contribute not only to cellular evolution and genetic diversity but also to mutation and disease. In order to study these effects in detail, a number of programs and databases have been developed to assist in discovery and annotation of inverted repeats in various genomes.