Imaging mass spectrometry (IMS) has been developed as a method for determining and visualizing the distribution of proteins and lipids across sections of dissected tissue. Although lipids play an important role in mammal development, their detailed distributions have not been analyzed by conventional methods. In this study, we tried to determine and visualize lysophosphatidylcholine (LysoPtdCho) and triacylglycerol (TAG) in a mouse embryo by matrix-assisted laser desorption/ionization (MALDI) hybrid quadrupole time-of-flight (TOF) mass spectrometer. Many peaks were detected from a raster scan of the whole embryonic sections. The peaks at m/z 496.33, 524.36, 879.72, 881.74, and 921.74 were identified by MS/MS analyses as [LysoPtdCho (16:0) + H]+, [LysoPtdCho (18:0) + H]+, [TAG (16:0/18:2/18:1) + Na]+, [TAG (16:0/18:1/18:1) + Na]+, and [TAG (16:0/20:3/18:1) + K]+, respectively. The ion images constructed from the peaks revealed that LysoPtdCho were distributed throughout the body and TAGs were distributed around the brown adipose tissue and in the liver at embryo day 17.5. Thus, IMS system based on MALDI hybrid quadrupole TOF MS revealed the distribution of LysoPtdCho and, more importantly, the organ-specific distribution of TAGs in the embryonic stages of mammals for the first time. We can conclude that this technique enables us to analyze the roles of various lipids during embryogenesis and gives insight for lipid research.