Polytene chromosomes are giant chromosomes common to many dipteran (two-winged) flies. They begin as normal chromosomes , but through repeated rounds of DNA replication without any cell division (called endoreplication), they become large, banded chromosomes.

Polytene chromosomes are usually found in the larvae, where it is believed these many-replicated chromosomes allow for much faster larval growth than if the cells remained diploid. Simply because each cell now has many copies of each gene, it can transcribe at a much higher rate than with only two copies in diploid cells.