Objective To investigate the clinical and EEG characteristics, therapeutic response and prognosis in children with atypical absence seizures. Methods The clinical and EEG data of 43 children with atypical absence seizures in Qilu Hospital, Shandong University during January 2011 to December 2016 were analyzed, and therapeutic response and prognosis were followed up. Results Childre were 24 male and 19 female with the mean age of 5.43 y. The onset ages were from 1 years and 8 months to 10 years and 3 months. All of the 43 patients had MRI examines, and 18 children were normol. MRI abnormalities appeared in 25 children, including cerebral cortical dysplasia and cerebral atrophy (13 cases), congenital corpus callosum hypoplasia (2 cases), and abnormal signal in bilateral posterior putamen (2 cases), encephalomalacia focus(4 cases), ventricle expention (2 cases), hydrocephalus(2 cases). All the children underwent EEG more than once. All children had atypical absence seizures during daytime. Children had slowly backgrounds in retesting EEG, and spine and slow waves of 1.5 Hz to 2.8 Hz could be seen in all the atypical absence seizures. All children were followed up, and except 6 children with complete control, 19 children’ parents reported seizure- free, 18 children have poor effect. Forty Children had various degrees of psychological abnormalities and motor regression. Among them 13 cases had psychological abnormalities and motor regression before disease; cognitive ability of 27 cases were normal before onset age, however, about 75% to 95% of the children became abnormal 2 years after atypical absence seizures. The rest 3 cases had no obviously impairment. Conclusions Most of the atypical absence seizures children had small onset age and high incidence in mental damage and cognitive impairment. The course of typical absence seizures aggravate gradually, and often develops to nonspecific brain damage in this process. Antiepileptic drugs can reduce the frequency of the seizure in part of the patients, but had no effect on psychological and motor regression.