Iodine deficiency disorders (IDD) affect millions of people in developing countries mainly due to dietary iodine deficiency and aggravating factors that affect the bioavailability of iodine in the body. Iodine deficiency disorder is one of the public health problems of Ethiopia. Recent findings show that both endemic and nonendemic areas have high goiter rates. Burie and Womberma districts are two of the endemic goiter areas in the country. The etiology of goiter in these areas is not fully studied so far. The objective of this cross-sectional community based study was to assess the magnitude and causes of goiter. The study was conducted in July 2010. The sample size was determined by assuming 50% prevalence of total goiter rate, 5% error, 95% confidence interval, design effect of 1(random) and 5% of non-response rate. A two-stagerandom sampling (sub-district and village) was used to select children aged 6-12 years and their biological mothers from10 randomly selected villages in each of the districts. Overall, 403 households participated in the study. The assessment was conducted using palpation of thyroid size, urinary iodine level determination, household level interview and Focus Group Discussion (FGD). The study revealed a total goiter prevalence rate of 54% and 30.1% in children and their biological mothers, respectively. More than 64% of the children were severely iodine deficient. The major cause for goiter as revealed by urinary iodine level and concentration of iodized salt is dietary iodine deficiency. There are no goitrogenic foods such as cassava; however, goitrogenic chemicals such as Dichlorodiphenyltrichloroethane (DDT) and 2,4-Dichlorophenoxyacetic acid (2,4-D) were widely used. The study areas are known for surplus produce of cereals, legumes and chilli. In order to reverse the problem, immediate and sustainable distribution of iodated salt/oil capsule, prohibition of direct application of pesticides on foods and awareness creation on adverse effects of IDD and benefits of iodine nutrition is highly recommended.