Polygalacturonase-inhibitor proteins (PGIPs) are plant cell wall glycoproteins, involved in the inhibition of microbial endo-polygalacturonases (EPGs). The present study involved activity guided partial purification of pearl millet [Pennisetum glaucum (L.) R.Br.] protein extract by cation exchange chromatography, which resulted in two pooled protein peaks -Peak-A and Peak-B, both of which showed inhibitory activity against the Aspergillus niger EPG. Protein separation of the two peaks by gel electrophoresis showed prominent bands between 29 and 43 kDa, consistent with the molecular weights of the known plant PGIPs. The two PGIP peaks were further studied for their inhibitory activities with respect to three parameters viz., inhibitor concentration, pH and temperature effects. Enzyme inhibition was partial and increased with inhibitor concentration. The Peak-B was found to be the more active inhibitor of the two. The results indicate the presence of at least two isoforms of PGIP in pearl millet. This is the first such study to be undertaken in understanding the presence of the PGIPs in millets.