Bacterial endotoxins or lipopolysaccharides (LPS) are among the most potent activators of innate immune system, yet mechanisms of their action and, in particular, the role of the glycans remain elusive. Efficient noninvasive labeling strategies are necessary for studying interactions of LPS glycans with biological systems. Here, we describe a new method for labeling LPS and other lipoglycans with luminescent quantum dots (QDots). The labeling is achieved by the partitioning of hydrophobic quantum dots into the core of various LPS aggregates without disturbing the native LPS structure. The biofunctionality of the LPS-QDot conjugates is demonstrated by labeling of mouse monocytes. This simple method will find broad applicability in studies concerned with visualization of LPS biodistribution and identification of LPS-binding agents.