Purpose To evaluate and compare the results of puncture, aspiration, injection and re-aspiration (PAIR) and catheterization techniques for treatment of CE1 and CE3a liver hydatid cysts according to World Health Organization classification. Materials and Methods Forty patients (29 females) with 56 liver CE1and CE3a cysts were prospectively randomized and enrolled into 2 groups by sealed envelope method. Procedures were performed under general anesthesia. Several parameters including technical success (completing procedure steps), clinical success (lack of recurrence on follow-up), major and minor complications, long-term changes of cyst cavities and length of hospital stay were compared between two groups. Results As in 2 patients with 3 cysts, PAIR technique had to be changed to catheterization technique due to technical reasons. The technical success rates were 91.9% and 100% for PAIR and catheterization groups, respectively. Volume decrease rates were 78.5% and 86.8% in PAIR and catheterization groups, with a mean follow-up of 78.1 and 71 months, respectively. There was no mortality, anaphylactic shock or intraabdominal dissemination. The rate of major complications such as abscess, cysto-biliary fistula and recurrence was 2.94% and 36.84% in PAIR and catheterization groups, respectively (p = 0.002). Median length of hospital stay was shorter in PAIR group (1 vs 4 days) (p = 0.015). Conclusion PAIR technique should be preferred to catheterization technique for treatment of liver CE1 and CE3a cysts due to lower rates of major complications and length of hospital stay. Catheterization technique should be employed when cysto-biliary fistula was evident.