This study aimed to clarify the mechanism of the spacing of murine embryos along the metrial and anti-metrial (MA) axis of the uterus using our newly developed experimental model. The model mice were produced by keeping mice in the supine position from the pre-implantation to implantation period. The starting points and periods of restraint of the mice in the supine position were set variously during the peri-implantation. Then, the position of the embryo was evaluated morphologically. In only one group (set in the instrument from the second day of pregnancy, Day 2, to Day 5), strong disruption of embryo spacing along the MA axis was observed. On the other hand, there was little abnormality in embryo positioning in the groups that were treated from Day 3 to Day 5 or from Day 3 to Day 6. These results suggested that determination of the position of the embryo in the MA axis is not related to duration of the experiment (2 days or 3 days), but is related to the starting time-point of the experiment, at Day 2 or Day 3. In conclusion, the period between Days 2 and 3 is critical for determination of the position of the embryo along the MA axis.