The Workshop on Logic and Systems Biology is affiliated with the 2006 Federated Logic Conference (FLoC) in Seattle, Washington. An essential feature of this workshop is that it brings together people from different disciplines: biology, computer science, and mathematics. Although these different areas have impacted each other often in the past, not all the researchers in a given field are fully aware of the recent advances in the other ones. This workshop will focus on the connections between molecular biology, logic, and formal methods in computer science. One goal of this conference is to introduce systems biology to members of the FLoC community. This is a very new direction for computer science and logic, and although there is a high level of interest in the subject, most attendees of the FLoC are not very familiar with it. Another goal is to foster a dialogue between researchers in systems biology and computer science, with the hope that this will encourage collaborations between the two groups, leading to new applications of logic and raising interesting theoretical questions. Therefore the lectures are intended to be accessible to biologists and FLoC attendees. A third goal of the meeting is to help students, in particular graduate students and recent Ph. D.s, become acquainted with these areas of research. We hope this will broaden their perspective and will contribute to their research and teaching careers.