To determine if the prevalence of non- albicans Candida spp. has increased at two institutions in Israel, the distribution of 6,954 Candida isolates obtained from sterile and nonsterile sites during the periods 1995-1996 and 1999-2000 were compared. In the latter period, a slight decrease was observed in the prevalence of non- albicans Candida spp. isolated from sterile sites (from 39% to 37%) and nonsterile sites (from 38% to 35%). Specifically, the prevalence of Candida glabrata increased significantly in sterile sites, from 26% to 35% (P=0.0095), and in nonsterile sites, from 18% to 27% (P<0.0001), and the prevalence of Candida krusei increased significantly in sterile sites, from 2% to 7% (P=0.0072). The prevalence of Candida parapsilosis decreased significantly in nonsterile sites, from 31% to 23% (P=0.0002). Continuous surveys of the distribution of Candida spp. and analysis of the clinical significance of changes are warranted.