The use of data from people with cognitive impairments to inform theories of cognition is an established methodology, particularly in the field of cognitive neuropsychology. However, it is less well known that studies that aim to improve cognitive functioning using treatment can also inform our understanding of cognition. This paper discusses a range of challenges that researchers face when testing theories of cognition and particularly when using treatment as a tool for doing so. It highlights the strengths of treatment methodology for testing causal relations and additionally discusses how generalization of treatment effects can shed light on the nature of cognitive representations and processes. These points are illustrated using examples from the Special Issue of Cognitive Neuropsychology entitled Treatment as a tool for investigating cognition.