As interest in the potential biomedical applications of carbon nanotubes increases, there is a need for methods that can image nanotubes in live cells, tissues and animals. Although techniques such as Raman, photoacoustic and near-infrared photoluminescence imaging have been used to visualize nanotubes in biological environments, these techniques are limited because nanotubes provide only weak photoluminescence and low Raman scattering and it remains difficult to image both semiconducting and metallic nanotubes at the same time. Here, we show that transient absorption microscopy offers a label-free method to image both semiconducting and metallic single-walled carbon nanotubes in vitro and in vivo, in real time, with submicrometre resolution. By using appropriate near-infrared excitation wavelengths, we detect strong transient absorption signals with opposite phases from semiconducting and metallic nanotubes. Our method separates background signals generated by red blood cells and this allows us to follow the movement of both types of nanotubes inside cells and in the blood circulation and organs of mice without any significant damaging effects.