Microglial cells are the resident immune cells of the central nervous system. Their function resembles that of tissue macrophages and, as such, they share many properties with both peripheral macrophages and monocytes. One striking similarity is the difficulty with which these cells can be genetically manipulated via transfection or transduction. We have sought to overcome this challenge and generate stably transduced microglial cell lines. Based on encouraging results from macrophages, we hypothesized that lentiviral vectors might provide a valuable tool in the transduction of microglial cells. Using a lentiviral‐based vector system expressing enhanced green fluorescent protein (eGFP) under the control of the murine stem cell virus promoter (MSCV), we found that multiplicities of infection (MOIs) of 1, 10, and 100 transduce >70%, >88%, and >95% of the cells, respectively. From the pool of transduced cells, we established lines of N9 and BV‐2 microglial cells with distinct fluorescence intensities. Using real time‐polymerase chain reaction (PCR), we correlated the integrated eGFP copy numbers to eGFP fluorescence measured by flow cytometry. When mixed, up to three lines with different eGFP intensities could be separated by flow cytometry and fluorescence microscopy. Neither infection nor transgene expression influenced microglial activation as assessed by nitric oxide (NO) production, cytokine release, and surface antigen expression. Our findings that microglial cells are easily transduced by lentiviral based vectors will facilitate research depending on genetic manipulation and help generate transgenic cell lines. In addition, the availability of microglial cell lines with defined fluorescence properties could replace elaborate staining procedures for microglial identification in co‐culture experiments. © 2004 Wiley‐Liss, Inc.