Hydatid disease is a parasitic disease that is treated primarily by surgery. The most important complication of surgical treatment is spillage of the contents of the cyst, leading to secondary dissemination. In this study, the effect of chlorhexidine gluconate (Chx-Glu) was investigated in the treatment of experimental intraperitoneal hydatidosis (IPH). IPH was reproduced in 100 Wistar albino rats by inoculation with 1 ml of a suspension contained approximately 1500 viable protoscolices of Echinococcus granulostis following determination of scolicidal activity of chlorhexidine gluconate in vitro. Five minutes after protoscolex inoculation, 5 ml of the scolicidal solution was instilled into the peritoneal cavity: 0.9% NaCl (control group), 4.0% Chx-Glu, 0.4% Chx-Glu, and 0.04% Chx-Glu. After 6 months of follow-up, the rats were sacrificed, and the number of isolated cysts, peroperative and postoperative deaths, and toxicity were evaluated. Cyst formation did not occur in any of the Chx-Glu groups compared to the control group (p < 0.05), whereas it was detected in all of the control rats. In addition, to 4.0% Chx-Glu was found to be more toxic and to cause a high mortality rate compared to the 0.4% and 0.04% Chx-Glu groups and the control group (p < 0.05). Chx-Glu 0.04% was found to be the most potent, nontoxic agent; it is easily available, inexpensive, and highly potent in a short period of time at the low concentration. Chx-Glu 0.04% can be used safely in the treatment of intraperitoneal hydatidosis and hydatid cyst.