The ability to detect HIV-1 in tissues that are not readily amenable to biopsy greatly limits the diagnosis and control of HIV infection, and ultimately, our ability to understand HIV-induced disease pathology. In view of this, we explored the utility of diagnostically measuring HIV-1 infection using 31P nuclear magnetic resonance (31P-NMR). 31PNMR enables the correlation of infection to changes in the concentration of specific intracellular metabolites, macromolecules and of bioenergetic parameters that are key to mammalian cell physiology. Examples include primary components of biological membranes such as phosphomonoester (PME) and phosphodiester (PDE) lipids. Using 31PNMR we found that changes in the ratio of PDE/PME in human cell lines and primary isolates were significantly altered following HIV-1 infection. Our findings showed that the ratio of cellular PDE/PME uniformly decreased 2.00 - 2.26 fold in HIV-1infected cells. Using the altered PDE/PME ratio as a selection criterion, we next assessed HIV-1 infection in lymphocytes isolated from both HIV-1 seropositive and non-infected human subjects. A decreased PDE/PME ratio was characteristic of HIV-1 infection in each instance. These results demonstrate that changes in cellular phospholipids induced during HIV-1 infection may be used to uncover basic mechanisms of HIV-1 pathology, and potentially, may be extrapolated to explore the application of NMR analysis as a technique for imaging infected organs and tissues in situ.