There is increasing interest in using exogenous labels such as bromodeoxyuridine (BrdU) or superparamagnetic iron oxide nanoparticles (SPION) to label cells to identify transplanted cells and monitor their migration by fluorescent microscopy or in vivo magnetic resonance imaging (MRI), respectively. Direct implantation of cells into target tissue can result in >80% cell death due to trauma or apoptosis. Bystander uptake of labeled cells by activated macrophages (AM) can confound the interpretation of results. This study investigated the frequency of BrdU or SPION uptake by AM using the Boyden chamber model of inflammation. SPION/BrdU-labeled bone marrow stromal cells or HeLa cells, AM, and mouse fibroblasts (MF) or human fibroblasts (HF) were mixed in various ratios in Matrigel in the upper chamber and incubated for up to 96 hours. The AM were chemotactically induced to migrate to the lower chamber. Fluorescence-activated cell sorting analysis of AM from lower and upper chambers, in the presence of either MF or HF using anti-CD68, anti-BrdU, anti-dextran antibodies, revealed 10%-20% dextran-positive or 10% BrdU-positive AM after 96 hours of incubation. Transfer of iron to AM accounted for <10% of the total iron in labeled cells. The uptake of BrdU and SPION was dependent on the ratio of labeled cells to inflammatory cells and microenvironmental conditions. Direct implantation of BrdU/SPION-labeled cells into target tissue can result in uptake of label by AM; therefore, care should be taken to validate by histology transplanted cells for bystander cell markers and correlation with MRI results.