The purpose of this study was to investigate the differences between technetium-99m ethyl cysteinate dimer ((99m)Tc-ECD) and technetium-99m hexamethylpropylene amine oxime ((99m)Tc-HMPAO) uptake in the same brains by means of statistical parametric mapping (SPM) analysis. We examined 20 patients (9 male, 11 female, mean age 62±12 years) using (99m)Tc-ECD and (99m)Tc-HMPAO single-photon emission tomography (SPET) and magnetic resonance imaging (MRI) of the brain less than 7 days after onset of stroke. MRI showed no cortical infarctions. Infarctions in the pons (6 patients) and medulla (1), ischaemic periventricular white matter lesions (13) and lacunar infarction (7) were found on MRI. Split-dose and sequential SPET techniques were used for (99m)Tc-ECD and (99m)Tc-HMPAO brain SPET, without repositioning of the patient. All of the SPET images were spatially transformed to standard space, smoothed and globally normalized. The differences between the (99m)Tc-ECD and (99m)Tc-HMPAO SPET images were statistically analysed using statistical parametric mapping (SPM) 96 software. The difference between two groups was considered significant at a threshold of uncorrected P values less than 0.01. Visual analysis showed no hypoperfused areas on either (99m)Tc-ECD or (99m)Tc-HMPAO SPET images. SPM analysis revealed significantly different uptake of (99m)Tc-ECD and (99m)Tc-HMPAO in the same brains. On the (99m)Tc-ECD SPET images, relatively higher uptake was observed in the frontal, parietal and occipital lobes, in the left superior temporal lobe and in the superior region of the cerebellum. On the (99m)Tc-HMPAO SPET images, relatively higher uptake was observed in the medial temporal lobes, thalami, periventricular white matter and brain stem. These differences in uptake of the two tracers in the same brains on SPM analysis suggest that interpretation of cerebral perfusion is possible using SPET with (99m)Tc-ECD and (99m)Tc-HMPAO.