This book constitutes the refereed proceedings of the Second International Conference on Foundations of Software Science and Computation Structures, FOSSACS '99, held in Amsterdam, The Netherlands in March 1999 as part of ETAPS'99. The 18 revised full papers presented were carefully selected from a total of 40 submissions. Also included are three invited papers. The central issues of the papers are theories and methods which suport the specification, transformation, verification and analysis of programs and software systems.