The human immunodeficiency virus type 1 (HIV-1) predominantly infects two main cell types: T-lymphocytes and monocyte-derived cells such as macrophages, dendritic cells, and Langerhans cells. Studies in patients aimed at uncovering and understanding the molecular mechanisms for viral persistence and latency in macrophages in particular are challenging because these cells reside in tissues and can only be extracted using invasive methods. The in vitro human monocyte-derived macrophage (MDM) model provides an amenable system to study HIV–host cell interactions at the molecular level. Infection of macrophages with a recombinant M-tropic virus that contains the green fluorescent protein (GFP) gene within its genome allows the detection of cells with integrated viral DNA that are producing viral particles. The infected cells can be studied at the single-cell level using a variety of fluorescence-based technologies such as flow cytometry, conventional and confocal microscopy, and laser capture microdissection.