Children with epilepsy are known to have high rates of mental health problems. The role of seizures in the development of these problems is not known primarily because of difficulties in separating the effects of seizures from the three other potential causal factors: (a) poor child and family response to the condition, (b) side effects of antiepileptic medication, and (c) neurological dysfunction that causes both the seizures and the behavioral problems. Although cross-sectional studies focusing on children with chronic epilepsy show associations between behavior problems and each of these causal factors, it is not possible to isolate the effects of any one causal factor using this design. A stronger approach is to conduct prospective studies of children with new-onset seizures. Recent research on children with new-onset seizures suggests that side effects of antiepileptic medication and poor child and family response do not play major roles in the development of behavior problems. Results from a prospective study in children with new-onset seizures show an association between seizures and behavior problems. Separating effects of seizures from effects of neurological dysfunction on behavior problems, however, will be difficult even in prospective studies of children with new-onset seizures. Transient cognitive impairment (TCI) from interictal epileptiform discharges is proposed as an alternative explanation for behavior problems.