To compare natural course and treatment results of various types of choledochal cysts. Complication rate in treated (T) and natural course in not treated (NT) patients with choledochal cysts were compared. The level of bilioenteric anastomosis after cyst resection was categorized and their post-procedure courses were analyzed. A total of 204 patients (T, 174; NT, 30) were included. Patients with initial malignancies were excluded from the outcome analysis (n = 13). Of the remaining 191 patients, the mean follow-up time was 35.9 months (range 6-310.7 months). Biliary stricture was the most troublesome post-operative complication, and occurred in 10 patients (6.1%). It occurred significantly more frequently in the above hilar anastomosis group than in at or below (p-trend = 0.017), and also with older age (p-trend = 0.019). Common bile duct stone was the most frequent adverse event among NT (42.9%). Overall, there were fewer complications among treated patients (T, 17.2%; NT, 67.9%; p < 0.001). Anomalous pancreaticobiliary union (APBU) was present in 69 patients (37.5%), which was associated with higher prevalence of carcinoma (APBU-present, 13%; APBU-absent, 3.5%; p = 0.019). No malignancy developed in both T and NT groups during follow-up. This study suggests, that even asymptomatic choledochal cysts should be treated, not only for prevention of malignancies, but also to lower the future adverse events. Bilioenteric anastomosis at larger caliber duct is recommended for prevention of post-operative biliary strictures.