Nuclear magnetic resonance (NMR) microscopy is a magnetic resonance imaging method with enhanced spatial resolution due to the use of a high static magnetic field and high magnetic field gradients. It is considered to be a useful tool for non-invasive and continuous investigation of tissue and organs at the histological level. In this study, we applied NMR microscopy to assessment of morphology in mouse embryos using a developmental disorder model induced by retinoic acid administration. Pregnant mice were given 50 mg/kg all-trans retinoic acid at 8.5 dpc. Embryos were collected at several time points after treatment and examined by NMR microscopy after fixation. Two-dimensional and three-dimensional spin echo sequences were used. Tissue contrast on two-dimensional images changed according to length of repetition time and echo time. and also to developmental stage of embryos. Two-dimensional and three-dimensional images nondestructively demonstrated defects in development of the skeleton and soft tissue, e.g. hypoplasia of vertebrae in the lumbar and tail regions and dysplasia of the spinal cord. in embryos exposed to retinoic acid. These morphological abnormalities were confirmed by conventional assessment after imaging. Although further improvements are required, NMR microscopy will provide a new approach for multi-parameter assessment of embryonic development under physiological and pathological conditions.