In Chapter 7, longitudinal data analysis with a dichotomous outcome variable is discussed. The discussion includes simple methods such as the change in proportions, the McNemar test and Cochrane’s Q as well as regression-based methods such as logistic mixed model analysis and logistic GEE analysis. An important part of this chapter is related to the different results obtained from a logistic GEE analysis and a logistic mixed model analysis. The difference is caused by the fact that GEE analysis is a population average approach, while mixed model analysis is a subject-specific approach. This difference has no influence on the results of a linear mixed model or GEE analysis, but has influence on the results of a logistic mixed model or GEE analysis. It is shown that the results obtained from a logistic GEE analysis are more valid than the results obtained from a logistic mixed model analysis. Also in this chapter, all methods are accompanied by extensive real-life data examples.