The main purpose of this article is to point out common pitfalls that can confuse comparative analyses of indicators of perinatal health and to discuss ways to overcome or minimize these difficulties. The challenge is to distinguish 'real' variations in the value of an indicator from variations due to differences in registration practices and definitions and from random variation. The first section presents the major properties that are desirable in indicators of perinatal health status and perinatal health care in Europe to be used for comparative purposes. The second section provides specific examples of the types of methodological difficulties encountered in European cross-country comparisons due to variations in the definition, measurement and construction of indicators. The conclusion discusses the PERISTAT project's responses to these difficulties and how these methodological constraints impact on the selection of an appropriate indicator set for Europe today.