We hypothesized that prolonged bedside limited-channel amplitude-integrated electroencephalogram (aEEG) monitoring following a standard 1-hour conventional electroencephalogram (cEEG) would increase the detection of subclinical seizures and allow continuous evaluation of the background EEG in neonatal encephalopathy. This may identify complementary roles for these EEG technologies in neonatal units where continuous cEEG monitoring may not be readily available. We prospectively recruited 25 term neonates with a diagnosis of neonatal seizures or encephalopathy. All infants underwent a standard 1-hour cEEG followed by 12 to 24 hours of aEEG monitoring. Data from the aEEG (plus the raw signal) were analyzed by an epileptologist and compared with information obtained from the clinical report of the cEEG. aEEG and cEEG data were available for 24 infants. Results from magnetic resonance imaging (MRI) performed at 7 to 10 days of life were available in 23/24 infants. Background classification on cEEG and aEEG was similar in 83% of patients. Five of 24 infants had normal background on cEEG. Prolonged aEEG detected evolution of background from initially normal to moderately abnormal in an additional four infants. It also detected more subclinical seizures than the 1-hour cEEG in 8/14 infants. Normal background on aEEG and cEEG was associated with normal MRI results, and severe background abnormality (5/24) on both aEEG and cEEG was associated with abnormal MRI results. Data obtained from prolonged aEEG (plus raw EEG) provide similar background activity, enhance seizure detection, and complement standard cEEG in predicting short-term outcomes, based on MRI, in term neonates with seizures or encephalopathy. Limited-channel aEEG technology may provide a pragmatic alternative for longitudinal monitoring of newborn infants with encephalopathy in neonatal units where prolonged video EEG monitoring is not feasible.