OBJECTIVES Up to one-third of the children with epilepsy are diagnosed with cryptogenic localization related epilepsy (CLRE). As yet, there is a lack of studies that specify the short- and long-term prognosis for this group. In this study, we systematically established neurological outcome (represented by seizure frequency) as well as neuropsychological outcome in a cohort of 68 children with CLRE who had been referred to our tertiary outpatient clinic. Also, we analysed correlations with risk and prognostic factors. PATIENTS AND METHODS A systematic cross-sectional open clinical and non-randomized design was used including 68 children admitted to our epilepsy centre in a child neurological programme between January 1999 and December 2004. A model was defined, distinguishing risk factors with a potential effect on epileptogenesis (history of febrile seizures, family history of epilepsy, history of early mild development delay and serious diagnostic delay) and prognostic factors, with a potential effect on the course of the epilepsy (neurological symptoms or soft signs, age at onset, duration of epilepsy, seizure type, percentage of time with epileptiform activity, localization of epileptiform activity, treatment history and treatment duration). Seizure frequency was used as the primary outcome variable, whereas three neuropsychological outcomes (IQ, psychomotor delay and educational delay) were used as secondary outcome variables. RESULTS The children experienced a broad range of seizure types with the 'absence-like' complex partial seizure as the most commonly occurring seizure type. Almost half of the children of the study sample had a high seizure frequency. They experienced several seizures per month, week or even daily seizures. Also a substantial impact on neuropsychological outcome was observed. Mean full scale IQ was 87.7, mean academic delay was almost 1 school year and 27 children showed psychomotor delay on the Movement ABC. Only 'having more than one seizure type' showed a prognostic value for seizure frequency, and no factors were found to be correlated with the secondary outcome measures. None of the risk factors show a differential impact on seizure outcome. CONCLUSION CLRE has a non-predictable course; clinical variability is high and prognosis in many children with CLRE is obscure. Having more than one seizure type was the only factor correlated to seizure frequency. Further longitudinal studies are needed.