Recent advances in atlas-based analytic tools enables efficient and comprehensive analyses of entire mouse brains. However, these efforts focus almost exclusively on the adult mouse brain. Development represents a period of rapid and substantial brain reorganization, and brain anatomy at different developmental stages is markedly different from the adult state. Despite this knowledge, few three-dimensional brain atlases are available for the developing mouse brain, and none have been incorporated into tools and workflows for spatial registration and analysis of histological sections. We here present the Developmental Mouse Brain Atlases (DeMBA), a series of open-access, 3D reference atlases for four developmental stages of the postnatal mouse brain. The atlases were created by spatially transforming the adult brain segmentations of the Allen Mouse Brain Common Coordinate Framework (version 3, 2017 and 2022 editions) to a set of serial two-photon tomography templates of developing mouse brains publicly shared by Newmaster and colleagues1. DeMBA covers postnatal day 7, 14, 21 and 28 and are integrated into the suite of tools constituting the EBRAINS QuickNII-ilastik-nutil (QUINT) workflow. We demonstrate how these atlases can be used with the QUINT workflow to spatially register and analyze the number and distribution of labelled cells in microscopy images. DeMBA provides open-access 3D atlases, fully comparable with the adult Allen Mouse brain CCF v3, available for efficient integration and analysis of data from postnatal mouse brains. Funded from the European Union’s Research and Innovation Program Horizon Grant Agreement No. 101147319 (EBRAINS 2.0).1.Newmaster et al. Nat.Commun. (2020)