Abstract Thyroid hormone abnormalities are strongly associated with Down Syndrome (DS) with elevated thyroid stimulating hormone (TSH) levels as the most consistent finding. Using subtractive hybridization for gene hunting we found significant overexpression of mRNA levels for the TSH-receptor (TSH-R) in brain of a fetus with DS. Based upon this observation we determined TSH-R protein levels in five brain regions of patients with DS(n = 8), Alzheimer disease (AD, n =8) and controls (C, n = 8). Western blots revealed significantly elevated immunoreactive TSH-R protein(s) 40 kD and 61 kD in temporal and frontal cortex of patients with DS and, unexpectedly, in AD. Levels for the 40kD protein in temporal cortex were 1.00 ± 0.036 (arbitrary units ± SD) in C, 1.35 ± 0.143 in DS, 1.52 ± 0.128 in AD; in frontal cortex: 1.00 ± 0.046 in C, 1.10 ± 0.03 in DS, 1.10 ± 0.038 in AD. Levels for the 61 kD protein in temporal cortex were 1.01 ± 0.015 in C, 1.47 ± 0.013 in DS, 1.623 ± 0.026 in AD; in frontal cortex: 1.02 ± 0.020 in C, 1.18 ± 0.123 in DS, 1.48 ± 0.020 in AD. These results show that elevated brain immunoreactive TSH-R is not specific for DS and maybe reflecting apoptosis, a hallmark of both neurodegenerative disorders, as it is well-documented that the thyroid hormone system is involved in the control of programmed cell death.