Purpose: The aim of this study was to compare partial cystectomy and internal drainage of the cyst cavity with cystojejunostomy for the surgical treatment of giant hepatic hydatid cysts. Methods: Patients who underwent any type of surgical treatment between March 2009 and May 2013 for giant hepatic hydatid cysts were retrospectively evaluated. The data collected included demographic variables, diagnostic methods, surgical procedures, morbidity and mortality rates. Results: Twenty-eight patients who underwent surgery for giant hepatic hydatid cysts were included. There were 16 (57 %) female patients, with a mean age of 32.8 years. The diagnostic methods primarily included abdominal ultrasonography and computed tomography, which were performed in 62 % of the patients. The patients were divided into two groups with respect to the treatment modality: Group A (n = 13) treated with cystojejunostomy and Group B (n = 15) treated with partial cystectomy. The overall rate of cavity-related complications was 25 % in Group B, whereas none of the patients in Group A had a cavity-related complication during the follow-up period (p < 0.05). Conclusion: Cystojejunostomy is an effective and safe surgical approach for the treatment of giant hepatic hydatid cysts, with a lower rate of morbidity than partial cystectomy, and thus may be the surgical treatment of choice for giant hepatic hydatid cysts.