Microglial activation is emerging as an important etiologic factor and therapeutic target in neurodegenerative and neuroinflammatory diseases. Techniques have been lacking, however, for measuring the different components of microglial activation independently in vivo. We describe a method for measuring microglial proliferation rates in vivo using heavy water (²H₂O) labeling, and its application in screening for drugs that suppress neuro‐inflammation. Brain microglia were isolated by flow cytometry as F4/80⁺, CD11b⁺, CD45^low cells, and ²H enrichment in DNA was analyzed by gas chromatography/mass spectrometry. Basal proliferation rate was ∼1%/week and systemic administration of bacterial lipopolysaccharide (LPS) markedly increased this rate in a dose‐dependent manner. Induction of experimental autoimmune encephalomyelitis (EAE) in C57BL/6 mice by MOG_35–55 peptide stimulated proliferation of CD45^low microglia, which could be distinguished from the proliferation of CD45^high infiltrating monocytes. Minocycline (45 mg/kg/day, i.p.) inhibited resident microglial proliferation in both the LPS and EAE models. Thirteen drugs were then screened for their ability to inhibit LPS‐stimulated microglia proliferation. Female C57BL/6 mice were given LPS (1 mg/kg), and concomitant drug treatment while receiving ²H₂O label for 7 days. Among the drugs screened, treatment with isotretinoin dose‐dependently reduced LPS‐induced microglial proliferation, representing an action of retinoids unknown previously. Follow‐up studies in the EAE model confirmed that isotretinoin not only inhibited proliferation of microglia but also delayed the onset of clinical symptoms. In conclusion, ²H₂O labeling represents a relatively high‐throughput, quantitative, and highly reproducible technique for measuring microglial proliferation, and is useful for screening and discovering novel anti‐neuroinflammatory drugs. © 2007 Wiley‐Liss, Inc.