In vivo molecular imaging is a powerful tool to analyze the human body. Precision medicine is receiving high attention these days, and molecular imaging plays an important role as companion diagnostics in precision medicine. Nuclear imaging with PET or SPECT and optical imaging technologies are used for in vivo molecular imaging. Nuclear imaging is superior for quantitative imaging, and whole-body analysis is possible even for humans. Optical imaging is superior due to its ease of use, and highly targeted specific imaging is possible with activatable agents. However, with optical imaging using fluorescence, it is difficult to obtain a signal from deep tissue and quantitation is difficult due to the attenuation and scattering of the fluorescent signal. Recently, to overcome these issues, optoacoustic imaging has been used in in vivo imaging. In this article, we review in vivo molecular imaging with nuclear and optical imaging and discuss their utility for precision medicine.