The central hypothesis of this paper is that there may be situations in which the traditional approach to institutional analysis is of limited applicability. Such an approach, which has been called 'comparative institutional analysis', consists of comparing institutional environments and institutional arrangements in terms of specific economic or other efficiency criteria to see which one performs better. However, because of limitations to accurately predict the future performance of alternative institutional settings, comparisons are not always possible. Furthermore, in most cases the only information available is the performance of the current institutional setting. To account for this methodological deficiency, a generic methodology for institutional analysis, which consists of four steps (institutional structure, institutional efficiency, institutional choice, and institutional change), is proposed in this paper. Accordingly, the emphasis switches from evaluating alternative institutional choices to improving current scenarios. To show the validity of this methodology, some results of its application to a case study are presented. Although more research on this four-step methodology is needed, it proved to be robust when applied to the analysis of the governance of irrigated agriculture in the Peninsula of Santa Elena, Ecuador.