•Fresh organ dissection in young mice gives better results than fixing whole carcass.•Modified Davidson’s better than formalin or Bouin’s in fixation of juvenile brain.•The sequence of events during organ development is very similar in mice and rats.•Developmental milestones often achieved earlier in the mouse than in the rat. There is a growing demand for wild type mice and mouse models of disease that may be more representative of human conditions but there is little information on neonatal and juvenile mouse anatomy. This project produces sound and comprehensive histology background data on the developing neonatal mouse at different time points from Day 0 until Day 28. The work describes optimal methods for tissue harvesting, fixation and processing from the neonatal and juvenile mice which can be used in routine toxicology studies. A review of the available literature revealed inconsistencies in the developmental milestones reported in the mouse. Although it is true that the sequence of events during the development is virtually the same in mice and rats, important developmental milestones in the mouse often happen earlier than in the rat, and these species should not be used interchangeably.