This report presents an overview of methodological issues in estimating the indirect workplace costs of illness from data obtained in employee surveys using the World Health Organization Health and Work Performance Questionnaire (HPQ). The HPQ is a brief self-report questionnaire that obtains three types of information: screening information about the prevalence and treatment of commonly occurring health problems; information about three types of workplace consequences (sickness absence, presenteeism, and critical incidents); and basic demographic information. The report considers two sets of methodological issues. The first set deals with measurement. The rationale for the HPQ approach to measurement is described in this section. In addition, data are presented regarding the accuracy of HPQ measures, documenting that the HPQ has excellent reliability, validity, and sensitivity to change. The second set of methodological issues deals with data analysis. A number of analysis problems are reviewed that arise in using self-report nonexperimental survey data to estimate the workplace costs of illness and the cost-effectiveness of treatment. Innovative data analysis strategies are described to address these problems.