Napier stunt disease (NSD) is a threat to Napier grass farming in the smallholder dairy industry in east and central Africa. NSD in Kenya is caused by Candidatus Phytoplasma oryzae (Ns-phytoplasma) belonging to the 16SrXI group; vectored by a leaf hopper Maiestas banda. The objective of the study was to determine the incidence (proportion of diseased leaves) and severity (proportion of leaf area diseased [PLAD]) of stunt disease in Napier clones by screening in Bungoma, Kakamega and Busia Counties in Western Kenya. The Napier clones were germplasm collections maintained at KALRO Kitale and Muguga nurseries and in farmers’ fields. Data were collected from twenty farmers’ open fields and eighteen Napier clones were planted in a replicate per farm. A total of 360 (n) observations were done within the Counties in 2013. Five cuts were done and each cut was done every eight weeks at each farm. Low stunt disease severity with mean PLAD of 0.084 (n=126) and low disease incidence with mean of 0.008 was observed in Kakamega county. This showed that there were few new infections in the farmers sites. Low severity with mean PLAD of 0.002 (n=126) and high stunt disease incidence with mean of 0.047 was observed in Bungoma county. Low severity was attributed to soils high in humus. Higher severity with mean PLAD of 0.408 (n=108) and high incidence with mean of 0.101 was observed in Busia county with songor and the farmer clones having high disease Incidence. The severity and incidence were attributed to a high exchange rate of the planting materials within Busia County and across border exchange. The Napier clones with the lowest incidences and severity indices after five cuts can be multiplied using either clonal or micro-propagation methods to supply to farmers