Head smut caused by Tolyposporium penicillariae Bref. is a devastating fungal disease that cause up to 30% yield losses in pearl Millet (Pennisetum glaucum (L.) R.Br.). An experiment was carried out in two sites (Koibatek and Marigat) in Kenya to estimate the losses in grain yield due to head smut at varying levels of susceptibility in 50 promising advanced pearl millet genotypes. The test germplasm were planted in a complete randomized block design (RCBD) in three replicates during the short rains (Sept-Dec 2011) and long rains (April-July 2012). To assess the yield loss, two experiments were set as sprayed with fungicide to control disease and unsprayed. Results showed that among the tested genotypes, KAT PM1 and ICMV 221 were resistant checks and showed minimum yield loss as compared to the susceptible genotypes, (SDMV 94001 and SDMV 94014)