Abstract Given the increasing interest in understanding in vivo migration of different cell types, it would be useful to have a simple method for tracking multiple cell populations in animals. Here we evaluated near infrared (NIR) dyes that intercalate into cell membranes as cell tracking labels, using both high-throughput and high-resolution methods. We tracked cells in tissues containing significant autofluorescence. CellVue Burgundy (ex 683/em 707) and CellVue NIR815 (ex 786/em 814) are especially useful because their spectral properties match the laser and detectors of the LI-COR laser scanner. After labeling cells ex vivo and injecting them into tumor-bearing mice, the distribution of cells in tumor and organs could be quantified in tissue sections with high throughput by scanning many slides at once. For example, we compared brain tumor infiltration and organ distribution of naïve and activated lymphocytes in single animals. High-resolution microscopic examination of the same tissues could be done by a relatively inexpensive modification of an epifluorescence microscope using a custom designed diode laser light source. Light emitting diodes that emit 685 nm and 780 nm light allowed microscopic visualization of the NIR labeled cells in tissues. The NIR dye-labeled cells were visualized with a greater signal/noise ratio compared to visible wavelength dyes such as CFSE, because of the low levels of autofluorescence in the NIR range. We also describe a simple modification of immunohistochemical procedures that allows combined visualization of the hydrophobic NIR dyes and antibody probes of cell markers in unfixed tissue. In combination these techniques will facilitate cell tracking in vivo.