Joubert syndrome (JS) is a rare autosomal recessive disorder with key finding of molar tooth sign (MTS) on axial magnetic resonance images (MRI). Six phenotypic subgroups are known in JS: Pure JS, JS with ocular defect, JS with renal defect, JS with oculo renal defects, JS with hepatic defect, and JS with orofaciodigital defects. We are reporting a case of 14-year-old boy, who presented with oculoorofaciodigital defect (polydactyly, syndactyly, ankyloglossia, ptosis, retinal dystrophy) with endocrinopathy (gynecomastia, micropenis, low testosterone) and MRI suggestive of MTS. Such kind of oculo-orofaciodigital defect with endocrinopathy (without puebarche, thalarche and menarche until the age of 17 years with hormonal disturbance) was also found in his elder sister. JS with endocrinopathy is a rare presentation, this is either expansion of the spectrum of JS in Indian people or a combination with endocrinopathy can evolve in later age.