Intravital imaging is essential to explore immune cell dynamics, however, accessible penetration depths in lymphoid tissues are insufficient due to scattering. We demonstrate three-photon microscopy (3PM) in the marrow of mouse tibias, in spleens and lymph nodes, after excitation up to 1,700 nm wavelength, to track fluorescence and higher harmonics signals. 3PM enabled dynamic imaging, at sub-cellular resolution, more than three times beyond the penetration depth of two-photon microscopy.