We used a rat model of focal cerebral ischaemia to compare stimulated-echo (STE) and spin-echo (SE) echo planar (EPI) diffusion-weighted sequences as regards image quality and accuracy of calculation of apparent diffusion coefficients (ADC). Focal cerebral ischaemia was induced by endovascular occlusion of the middle cerebral artery in five rats. MRI was performed on a 2.35 tesla imager. For diffusion-weighted imaging (DWI) we used STE-EPI and SE-EPI with different diffusion times (delta) of 15, 30, 45, 60, 75 and 90 ms using values of b of 200, 300, 400, 500, 600 and 700 s/mm2. We assessed image quality, the signal-to-noise-ratio (SNR) and the accuracy of the ADC calculated from both sequences. Infarcts were delineated in all cases, independent of sequence type and delta. The image quality and SNR of the SE-EPI images were significantly better, with a higher SNR than STE-EPI images for short and intermediate values of delta. However, when delta reached 75 ms STE-EPI became superior to SE-EPI. ADC calculated from STE-EPI images were smaller than those from SE-EPI images for short and intermediate diffusion times, possibly because of the lower SNR of the former. We suggest that SE-EPI sequences be used for DWI of the brain, particularly on experimental systems and whole-body imagers with enhanced gradient hardware, where it is possible to run highly diffusion-weighted sequences (b > 500 s/mm2) with delta less than 50 ms. However, when using very long values of delta because of hardware restrictions or for measurement of restricted diffusion, STE sequences give better results.