Selection of cells positive for aldehyde dehydrogenase (ALDH) activity from a green-fluorescent background is difficult with existing reagents. Here we report a red-shifted fluorescent substrate for ALDH, AldeRed 588-A, for labelling viable ALDH(pos) cells. We demonstrate that AldeRed 588-A successfully isolates ALDH(hi) human haematopoietic stem cells from heterogeneous cord blood mononuclear cells. AldeRed 588-A can be used for multicolour applications to fractionate ALDH(pos) cells in the presence of green fluorophores including the ALDEFLUOR reagent and cells expressing enhanced green-fluorescent protein (eGFP). AldeRed 588-A stains ALDH(pos) murine pancreatic centroacinar and terminal duct cells, as visualized using fluorescent microscopy. AldeRed588-A provides a useful tool to select stem cells or study ALDH within a green-fluorescent background.