Thermal analysis is crucial for determining the propagation of heat and tracking the formation of hot spots in advanced integrated circuit technologies. At the core of the thermal analysis for integrated circuits is the numerical solution of the heat equation. Prior academic thermal analysis tools typically compute temperature by applying finite difference methods on uniform grids with time integration methods having fixed time step size. Additionally, the linear systems arising from the discretized heat equation are solved using direct methods based on matrix factorizations. Direct methods, however, do not scale well as the problem size increases. Moreover, most of the tools support only 2-D or a limited number of 3-D technologies. To address these issues, this paper presents a novel thermal analyzer with the ability to model both 2-D and 3-D circuit technologies. The analyzer solves the heat equation using the finite element method for the spatial discretization coupled with implicit time integration methods for advancing the solution in time. It also offers fully adaptive spatio-temporal refinement features for improved accuracy and computational efficiency. The resulting linear systems are solved by a multigrid preconditioned Krylov subspace iterative method, which gives superior performance for 3-D transient analyses. The analyzer is shown to accurately capture the propagation of heat in both the horizontal and vertical directions of integrated systems.