Polytene chromosomes exhibit intricate higher order chromatin structure that is easily visualized due to their precisely aligned component strands. However, it remains unclear if the same factors determine chromatin organization in polyploid and diploid cells. We have analyzed one such factor, the cell cycle, by studying changes in Drosophila nurse cell chromosomes throughout the 10 to 12 endocycles of oogenesis. We find that nurse cells undergo three distinct types of endocycle whose parameters are correlated with chromosome behavior. The first four endocycles support complete DNA replication; poorly banded polytene euchromatin progressively condenses during the late S phases to produce blob-like chromosomes. During the unique fifth endocycle, an incomplete late S phase is followed by a mitosis-like state during which the 64C chromosomes dissociate into 32 chromatid pairs held together by unreplicated regions. All the subsequent endocycles lack any late S phase; during these cycles a new polytene chromosome grows from each 2C chromatid pair to generate 32-ploid polytene nuclei. These observations suggest that euchromatin begins to condense during late S phase and that nurse cell polytene chromosome structure is controlled by regulating whether events characteristic of late S and M phase are incorporated or skipped within a given endocycle.