The explosion in neuroscientific knowledge has profound implications for education, and we advocate the establishment of the new discipline of 'pedagogical neuroscience' designed to combine psychological, medical, and educational perspectives. We propose that specific learning disabilities provide the crucible in which the discipline may be forged, illustrating the scope by consideration of developmental dyslexia. Current approaches have failed to establish consensus on fundamental issues such as theoretical causes, diagnostic methods, and treatment strategies. We argue that these difficulties arise from diagnosis via behavioural or cognitive symptoms, even though they may arise from diverse causes. Rather than an inconvenience, variability of secondary symptoms within and across learning disabilities can inform both diagnosis and treatment. We illustrate how brain-based theories lead to radical restructuring of diagnostic methods and propose that there is an urgent need to develop genetic and brain-based diagnostic methods designed to lead to individually-appropriate remediation and treatment methods.