Abstract Many combinatorial optimization problems entail a number of hierarchically dependent optimization problems. An often used solution is to associate a suitably large cost with each individual optimization problem, such that the solution of the resulting aggregated optimization problem solves the original set of optimization problems. This paper starts by studying the package upgradeability problem in software distributions. Straightforward solutions based on Maximum Satisfifiability (MaxSAT) and pseudo-Boolean (PB) optimization are shown to be ineffective, and unlikely to scale for large problem instances. Afterwards, the package upgradeability problem is related to multilevel optimization. The paper then develops new algorithms for Boolean Multilevel Optimization (BMO) and highlights a number of potential applications. The experimental results indicate that algorithms for BMO allow solving optimization problems that existing MaxSAT and PB solvers would otherwise be unable to solve