Cerebral venous thrombosis (CVT) is rare and has a wide spectrum of symptoms, therefore it is difficult to diagnose. Thrombosis of the deep cerebral veins occurs very rarely: it has been reported that approximately 6% of patients with CVT have deep CVT, and the prognosis for patients with this condition is poor. CVT has been reported in association with dehydration, a hypercoagulable state, mastoiditis, tumour invasion of a venous sinus, use of oral contraceptives, pregnancy, puerperium, head trauma, vasculitis, and intracranial and systemic infections. However, in the literature, there are few reported cases of CVT in association with iron deficiency anaemia, especially in adults. We present here two patients with bilateral thalamic and basal ganglionic lesions due to thrombosis of the deep cerebral veins. Both of our patients had severe hypochromic microcytic anaemia due to iron deficiency, and both had a good prognosis after 2 months.