Cryo-electron microscopy is playing a key role in the understanding HIV-1 infection and development of new drugs and therapeutic strategies for HIV-1 prevention and treatment. Over the past decade we have made a significant progress in determining structural mechanisms of HIV-1 capsid assembly, disassembly, maturation, and interactions with many host factors, through developing cutting-edge cryoEM technologies that bring unprecedented resolution and enable in situ structures of large assemblies and complexes in their native cellular environment. We use an integrative approach combining structural methods with retrovirology, cell biology and computer simulations, to better understand the infection process. Future cryoEM development, in particular on the correlative in situ microscopy, will allow us generate a framework for the development of new therapeutic interventions of HIV-1 and other pathogenic viruses.