The clinical manifestations of hydatidosis are various and related to anatomic location. Defining frequent symptoms and signs of the disease is imperative for early management of it. The aim of this report was to analyse the clinical features of infected children with hydatid cysts located in different organs. In this study, medical charts of 57 children between 3 and 16 years of age with hydatid cyst admitted to Pediatric Wards of Nemazee Hospital were evaluated over a 12 year period (from 2003 to 2014, prospectively). All the epidemiologic, clinical, paraclinical and therapeutic data were collected. The frequencies of hydatidosis in males and females were 42.1 and 56.1%, respectively. Hydatid cysts were found in the liver and lungs in 59.6 and 33.3% patients respectively and 2 patients had an asymptomatic cyst in the heart with concomitant liver and lung cysts. The right upper quadrant pain (100%) was the most common symptom in the liver cysts. Phlegm (78.9%), Dyspnea (57.9%), acute (47.4%) and chronic cough (47.4%) were mostly seen in lung hydatid cysts. Some symptoms such as fever (68.4%) and weakness (59.6%) were the most common presenting symptoms in both groups. All children were treated through surgical approaches plus medical treatment. In the present report, liver was the most common site of involvement in children. Liver hydatidosis should be considered in children with upper quadrant pain and pulmonary hydatidosis in children complaining of phlegm and dyspnoea.