Binding of Fru-2,6-P2 to yeast phosphofructokinase was investigated by ultrafiltration technique. Per mol of subunit of phosphofructokinase (M = 100,000) 0.5 moles of Fru-2,6-P2 are bound. The binding curve proceeds cooperatively (nH = 1.8 +/- 0.2). The apparent affinity constant of Fru-2,6-P2 amounts to about 2.25 +/- 0.12 microM. Fru-1,6-P2 decreases the affinity of yeast phosphofructokinase to Fru-2,6-P2. The data can be described by assuming either competition of Fru-2,6-P2 and Fru-1,6-P2 for the same binding site or conformationally mediated interactions.