Phase analysis is expected to improve the accuracy of myocardial ischemia diagnosis in conjunction with myocardial perfusion and wall motion imaging and quantification. Although previous studies have reported perfusion image disagreements in relation to radionuclides, a few reports have examined the influences of radionuclides on phase analysis. We evaluated the influences of different radionuclides on stress-induced left ventricular mechanical dyssynchrony by phase analysis using electrocardiogram (ECG)-gated myocardial perfusion single photon emission computed tomography (SPECT) (MPS) imaging in patients with ischemic heart disease (IHD). A total of 202 patients with suspected or known IHD were investigated retrospectively. All the patients underwent coronary arteriography and were subsequently classified into the following groups: 43 patients without any coronary lesion (0VD), 71 patients with single-vessel disease (1VD), 59 patients with two-vessel disease (2VD), and 29 patients with three-vessel disease (3VD). Both stress and rest gated-MPS were performed using 99mTc-methoxyisobutylisonitrile (MIBI)/tetrofosmin (TF) in 118 patients and with 201TlCl in 84 patients. Phase analysis was performed to obtain the peak phase, phase standard deviation (SD), and bandwidth. Finally, we investigated potential differences between the phase analysis indices and the respective radionuclides used. The peak phase did not exhibit any significant differences in the numbers of affected branches in either 99mTc-MPS or 201Tl-MPS during stress or rest MPS. Furthermore, both the phase SD and bandwidth demonstrated a tendency to increase in patients with increased numbers of affected branches. A significant difference was observed in the stress MPS when 99mTc-MIBI/TF was used (p < 0.05), but no significant difference was observed in the stress MPS when 201TlCl was used. Both the phase SD and bandwidth of all patients in 99mTc-MPS during stress were significantly larger than those at rest (p < 0.05). Conversely, both the phase SD and bandwidth of all patients in 201Tl-MPS at stress was significantly smaller than that at rest (p < 0.05). Phase analysis using 99mTc-MPS was considered to be useful for the detection of stress-induced left ventricular mechanical dyssynchrony, although it is necessary to be careful when using 201Tl-MPS.