To evaluate whether phase analysis imaging may predict treatment response and long-term prognosis after cardiac resynchronization therapy (CRT). Sixty-nine patients underwent myocardial perfusion imaging followed by CRT. Patients with ischaemic heart disease and non-ischaemic cardiomyopathy (NICM) were identified. Left ventricular (LV) mechanical dyssynchrony (LVMD) was assessed at phase analysis and the region of the latest mechanical activation was identified. LV pacing lead position was considered 'concordant' when located in the region of the latest mechanical activation, and 'discordant' otherwise. The '6 months post-CRT'/'baseline' ratio of LV ejection fraction was computed as a measure of CRT response. LVMD was revealed in 47/69 patients, 27 of whom (57%) had a concordant LV lead implantation. Only concordant pacing was associated with LV functional improvement (ejection fraction ratio: 1.28 ± 0.25 vs. 1.11 ± 0.32 in discordant stimulation, P = 0.028). However, this relationship persisted only in patients with NICM (P < 0.001), while it disappeared in those with ischaemic heart disease (P = NS). Twenty-eight events occurred during 30 ± 21 months follow-up. While discordant LV lead location was the major predictor of unfavourable prognosis (hazard ratio 3.29, 95% confidence interval 1.25-8.72; P = 0.016), this relationship was confirmed only in patients with NICM. Phase analysis of myocardial perfusion imaging may guide CRT implantation, identifying patients who would most likely benefit from this procedure.