Functional connectivity is altered in several mental disorders. We used resting-state functional MRI to examine the alterations in functional connectivity that occur in patients with absence epilepsy. We found an altered functional connectivity within and between functional modules in patients with absence epilepsy. Some brain regions had a greater number of altered connections. The functional connectivity within and between modules in absence epilepsy patients showed an increase in the number of positive connections and a decrease in the number of the negative connections. In particular, the superior frontal gyrus demonstrated both an increased number of connections with other nodes of the frontal default mode network and a decreased number of connections with the limbic system. These findings provide a new perspective and shed light on how the balance of connections within and between modules may contribute to the development of absence epilepsy. (C) 2012 Elsevier Ltd. All rights reserved.