<i>Background:</i> Considering that the incidence of dysphagia is as high as 55% following acute stroke, we undertook a systematic review of the literature to identify lesion sites that predict its presence after acute ischemic stroke. <i>Methods:</i> We searched 14 databases, 17 journals, 3 conference proceedings and the grey literature using the Cochrane Stroke Group search strategy and terms for MRI and dysphagia. We evaluated study quality using the Cochrane Collaboration’s risk of bias tool and extracted individual-level data. We calculated relative risks in order to model dysphagia according to neuroanatomical lesion sites. <i>Results:</i> Of 964 abstracts, 84 articles met the criteria for full review. Of these 84 articles, 17 met the quality criteria. These 17 articles dealt exclusively with dysphagia after infratentorial stroke and provided MRI correlates of dysphagia for 656 patients. The incidence of dysphagia according to stroke region was 0% in the cerebellum, 6% in the midbrain, 43% in the pons, 40% in the medial medulla and 57% in the lateral medulla. Within these regions, pontine (relative risk 3.7, 95% confidence interval 1.5–7.7), medial medullary (relative risk 6.9, 95% confidence interval 3.4–10.9) and lateral medullary lesions (relative risk 9.6, 95% confidence interval 5.9–12.8) predicted an increased risk of dysphagia. <i>Conclusions:</i> We sought to develop a neuroanatomical model of dysphagia throughout the whole brain. However, the literature that met our quality criteria addressed the MRI correlates of dysphagia exclusively within the infratentorium. Although not surprising, these findings are a first step toward establishing a neuroanatomical model of dysphagia after infratentorial ischemic stroke and provide insight into the assessment of individuals at risk for dysphagia.