Abstract. Atmospheric chemical transport models (CTMs) are essential tools for the study of air pollution, for environmental policy decisions, for the interpretation of observational data, and for producing air quality forecasts. Many air quality studies require sensitivity analyses, i.e., the computation of derivatives of the model output with respect to model parameters. The derivatives of a cost functional (defined on the model output) with respect to a large number of model parameters can be calculated efficiently through adjoint sensitivity analysis. While the traditional (first order) adjoint models give the gradient of the cost functional with respect to parameters, second order adjoint models give second derivative information in the form of products between the Hessian of the cost functional and a user defined vector.In this paper we discuss the mathematical foundations of the discrete second order adjoint sensitivity method and present a complete set of computational tools for performing second order sensitivity studies in three-dimensional atmospheric CTMs. The tools include discrete second order adjoints of Runge Kutta and of Rosenbrock time stepping methods for stiff equations together with efficient implementation strategies. Numerical examples illustrate the use of these computational tools in important applications like sensitivity analysis, optimization, uncertainty quantification, and the calculation of directions of maximal error growth in three-dimensional atmospheric CTMs.