Abstract Owing to “stacking” interactions certain positively charged dye molecules display biologically significant cooperative binding to single stranded polyanions. Temperature jump experiments with such systems reveal a peculiar slow relaxation process which cannot be ascribed to the actual binding reactions. In the special case of poly(glutamic acid) and acridine orange, light scattering measurements show it to be caused by a strong aggregation of the polymer-dye complexes depending primarily on the degree of binding. This effect is clearly reflected in changes of the visible absorption spectrum. Their wavelength dependences indicate that the aggregation is apparently associated with a spectral flattening as well as an enhanced binding of the dye which both result in a decrease of its absorbance. The thermodynamics and kinetics of the phenomenon can be understood on the basis of a simple model.