BACKGROUND: Fluorescent proteins such as GFP (Green Fluorescent Protein) and DsRED (Discosoma sp.Red Fluorescent Protein) are often used as reporter molecules for transgene expression in Drosophila and other species. We have recently reported methods that allow simultaneous tracking of animal movement and GFP expression in real time, however the assay was limited to single animals and a single transgene. Numerous studies would be facilitated by methods that allow for assay of multiple animals and multiple transgenes. FINDINGS: Here we report an improved fly video tracking system that allows multiple transgenic flies to be tracked simultaneously using visible light, GFP fluorescence and DsRED fluorescence. The movement of multiple flies could be accurately tracked at real time rates, while simultaneously assaying the expression level of two different transgenes marked with GFP and DsRED. The individual flies could be accurately tracked and distinguished even during periods when transgene fluorescence was undetected. For example, characteristic patterns of hsp70 and hsp22 transgene induction could be simultaneously quantified and correlated with animal movement in aging flies, and as groups of flies died due to dessication/starvation. CONCLUSION: The improved methods allow for more efficient assay of the correlation between gene expression, behavior, aging and mortality: multiple animals can be assayed with simultaneous quantification of multiple transgenes using GFP and DsRED fluorescence. These methods should allow for increased flexibility in experimental designs. For example, in the future it should be possible to use gene expression levels to predict remaining life span more accurately, and to quantify gene expression changes caused by interactions between animals in real time.