Hypothalamic hamartomas (HHs) are rare developmental malformations consisting of mixed neurons and glial cells, usually unilaterally attached to the tuber cinereum or mammillary bodies. We report on two patients, both suffering from pharmacoresistant epilepsy, behavioural and cognitive disturbances. Ictal and interictal electroencephalographic (EEG) abnormalities appeared bilaterally and multiregionally with right-sided preponderance. Magnetic-resonance imaging (MRI) revealed independent bilateral hypothalamic hamartomas, more prominently on the right side. Endoscopic surgery of the right HH was performed in each patient, resulting in a significant seizure reduction in both cases. To the best of our knowledge, there are no other reports of independent bilateral HHs in the literature.