We survey the evaluation methodology adopted in information extraction (IE), as defined in a few different efforts applying machine learning (ML) to IE. We identify a number of critical issues that hamper comparison of the results obtained by different researchers. Some of these issues are common to other NLP-related tasks: e.g., the difficulty of exactly identifying the effects on performance of the data (sample selection and sample size), of the domain theory (features selected), and of algorithm parameter settings. Some issues are specific to IE: how leniently to assess inexact identification of filler boundaries, the possibility of multiple fillers for a slot, and how the counting is performed. We argue that, when specifying an IE task, these issues should be explicitly addressed, and a number of methodological characteristics should be clearly defined. To empirically verify the practical impact of the issues mentioned above, we perform a survey of the results of different algorithms when applied to a few standard datasets. The survey shows a serious lack of consensus on these issues, which makes it difficult to draw firm conclusions on a comparative evaluation of the algorithms. Our aim is to elaborate a clear and detailed experimental methodology and propose it to the IE community. Widespread agreement on this proposal should lead to future IE comparative evaluations that are fair and reliable. To demonstrate the way the methodology is to be applied we have organized and run a comparative evaluation of ML-based IE systems (the Pascal Challenge on ML-based IE) where the principles described in this article are put into practice. In this article we describe the proposed methodology and its motivations. The Pascal evaluation is then described and its results presented.