Physical environmental cues signal cells to adapt according to their surroundings during physiological and developmental processes. One such environmental cue is the migration of cells through the network of confining intercellular tracks within the extracellular matrix. During this process of confined migration, cells must migrate through spaces with widths less than half the typical diameter of the largest organelle within the cell - the nucleus. This results in severe deformations of the nucleus and the chromatin contained within. In unconfined nuclei, it is well-established that chromatin is radially organized with “closed” heterochromatin more strongly associated with the nuclear periphery while “open” euchromatin is more associated with the nuclear interior. However, the effect of nuclear deformations on chromatin organization within subnuclear space, particularly during extended periods of confined cell migration, remains less understood. A major obstacle for these studies is the lack of easily implementable tools for visualizing confined cell migration in vivo. Here, we use the model of cell migration through in vitro PDMS microchannels to study the effects of confined cell migration on chromatin organization. These microchannels have defined widths of 3 µm and lengths of 150 µm to induce extended periods of nuclear deformation when cells migrate through. Using microscopy to visualize chromatin during confined migration, we observed that euchromatin and heterochromatin reorganize into distinct compartments along the longitudinal axis of cell migration. We have also analyzed the dynamics and molecular drivers of this confinement induced chromatin reorganization using biochemical and microscopy approaches. Our findings suggest that chromatin adopts a distinct non-radial organization during confined migration. Given the known role of chromatin architecture in regulating gene expression, we anticipate that this non-radial architecture could be a novel and important mechanical response of the cell to confinement. In the future, we aim to investigate how these structural changes in chromatin could functionally support confined cell migration.