The consequences of trypsin treatment of rabbit muscle phosphofructokinase, in terms of the physical and kinetic properties of the enzyme, have been investigated. At 1% trypsin (w/w) and 25 °C, no activity is lost over a period of 60 min. The complex sedimentation behavior at pH 8 (three peaks) is unchanged by this treatment as is the extent of dissociation of the enzyme when the pH is lowered from 8 to 6 or reassociation when the pH is raised back to 8. However, the trypsin-treated enzyme shows a subunit molecular weight, determined in the guanidine HCl or 0.5 m acetic acid, of 35,000-40,000 compared to the subunit molecular weight of the untreated enzyme at 75,000-80,000. Similarly, SDS gels give only a single species of about 80,000 for the native enzyme but two species, 42,000 and 48,000, for the trypsin-treated enzyme. Kinetic studies showed no differences in the regulatory properties of the enzyme including fructose 6-phosphate cooperativity, ATP inhibition, NH4+ activation, and cAMP activation. Small differences in stability and inhibition by citrate and creatine phosphate were observed.