Objective To study the pathogen distribution and drug sensitivity in childhood bacillary dysentery and to provide a basis for selecting antibiotics clinically.Methods A total of 290 children who were definitely diagnosed with bacillary dysentery by stool culture between 1998 and 2003 were eligible to this study.A drug sensitive test was performed by an improved Kirby-bauer method. Results Of the 290 cases, there were two types of positive bacterial species: Sh.sonnei (type D, n = 155) and Sh.flexneri (type B, n = 135).Between 1998 and 1999, Type Sh.flexneri was the main bacteria, while from 2000 through 2003, Type Sh.sonnei was predominant. Both Sh.flexneri and Sh.sonnei were sensitive to cefaclor, amikacin, gentamycin, and ceftriaxine, and insensitive to ampicillin and trimoxazole. Conclusions Types Sh.flexneri and Sh.sonnei bacteria were the major pathogen of childhood bacillary dysentery between 1998 and 2003. Cefaclor is an oral drug with few side effects, which can efficiently kill Shiga′s bacillus, and may be recommended in the treatment of this disorder.