Our goal in this work was to investigate the impact of CT-based attenuation correction on measurements of rat myocardial perfusion with (99m)Tc and (201)Tl single photon emission computed tomography (SPECT). Eight male Sprague-Dawley rats were injected with (99m)Tc-tetrofosmin and scanned in a small animal pinhole SPECT/CT scanner. Scans were repeated weekly over a period of 5 weeks. Eight additional rats were injected with (201)Tl and also scanned following a similar protocol. The images were reconstructed with and without attenuation correction, and the relative perfusion was analyzed with the commercial cardiac analysis software. The absolute uptake of (99m)Tc in the heart was also quantified with and without attenuation correction. For (99m)Tc imaging, relative segmental perfusion changed by up to +2.1%/-1.8% as a result of attenuation correction. Relative changes of +3.6%/-1.0% were observed for the (201)Tl images. Interscan and inter-rat reproducibilities of relative segmental perfusion were 2.7% and 3.9%, respectively, for the uncorrected (99m)Tc scans, and 3.6% and 4.3%, respectively, for the (201)Tl scans, and were not significantly affected by attenuation correction for either tracer. Attenuation correction also significantly increased the measured absolute uptake of tetrofosmin and significantly altered the relationship between the rat weight and tracer uptake. Our results show that attenuation correction has a small but statistically significant impact on the relative perfusion measurements in some segments of the heart and does not adversely affect reproducibility. Attenuation correction had a small but statistically significant impact on measured absolute tracer uptake.