Trends in the epidemiology of infections due to Shigella species over a period of 6 years (1986-1991) in Israel were studied by analysis of the results of 51,300 stool cultures, of which 2,987 yielded Shigella species. In a university hospital, the relative prevalence of Shigella sonnei in patients with shigellosis increased over the years from 60% in 1986 to 91% in 1991 (r = 0.93; P = .007); concomitantly, the prevalence of Shigella flexneri decreased from 29% to only 8% (r = -0.80; P < .05). In the community, the increase in prevalence of S. sonnei was more moderate and occurred only from 1989 to 1991. Since 1990, S. sonnei has been isolated from more hospitalized patients than has S. flexneri, in contrast to their rates of isolation in the past. The increase in prevalence of S. sonnei was most prominent among children, in whom it caused 94% of shigella infections in 1991. Shigella boydii and Shigella dysenteriae remained relatively rare, causing approximately 5% and approximately 1%, respectively, of the cases of shigella infection. Concomitantly, the antimicrobial resistance of S. sonnei has become significantly greater, and it is currently 2.7 and 1.6 times higher than that of S. flexneri to trimethoprim-sulfamethoxazole and ampicillin, respectively. We conclude that the relative frequency of S. sonnei is increasing, especially in hospitalized patients, and hypothesize that this may be related to its increasing antimicrobial resistance. These trends have clinical implications.