Hypothalamic hamartomas (HHs) are non-neoplastic mass lesions located in the hypothalamus that presented with central precocious puberty (CPP), and/or gelastic seizures. Seckel syndrome (OMIM210600, SCKL) is a rare autosomal recessive genetic spectrum disorder characterized by intrauterine growth retardation, proportionate osteodysplastic primordial dwarfism, a wide range of intellectual disability, "bird-headed" facial features and microcephaly with various brain structural abnormalities. Two siblings presented with a short stature with small head circumference and diagnosed SCKL 5. Interestingly, the younger sister had HH with CPP and a slipped capital femoral epiphysis during treatment. Herein, we report that the two siblings with the same genetic variant showed different phenotypes, which have not been reported previously as the first cases of SCKL diagnosed by genetic confirmation in Korea.