Single photon emission computed tomography (SPECT) using 99mTc-bicisate and N-isopropyl-p-[123I]iodoamphetamine ([123I]IMP) was compared in 25 patients suffering cerebral ischemia during the subacute phase (7-14 days) of stroke. Patients were classified as cortical strokes (15) and subcortical strokes (10) according to clinical and CT data. Images were analyzed by five independent blinded observers. Then, using a cross-matching method between normal and abnormal brain areas, we evaluated the sensitivity and specificity for 99mTc-bicisate and [123I]IMP and inter- and intraobserver reproducibility. A semiquantitative analysis was performed to compare abnormal hypoactive areas versus the corresponding contralateral areas for 99mTc-bicisate and [123I]IMP in the two patient groups. There was no significant difference for sensitivity and specificity between 99mTc-bicisate and [123I]IMP. Matching was approximately 90% in the two groups. The kappa-concordance index was satisfactory and slightly better for 99mTc-bicisate (0.485) than for [123I]IMP (0.435). Level of hypoactivity in the abnormal areas was significantly higher for 99mTc-bicisate (p < 0.03, n = 25) than for [123I]IMP, especially for cortical strokes. This comparative study demonstrates that 99mTc-bicisate is a very useful tracer for the detection of focal cerebral ischemia by SPECT during the subacute phase of stroke.