This is a comprehensive textbook specially written for undergraduate and graduate students in the biological sciences. The book is divided in two main sections. The first section addresses the principles behind gene expression studies, providing particular details on how to quantify gene expression from complex biofilm samples and reviewing the major problems and solutions commonly found when performing gene expression studies in biofilm samples. The second section focuses on the impact of pathogenic biofilms in human health and reviews how transcriptomic studies help unveil some of the mysteries behind biofilm pathogenicity.