Nonnegative and compartmental models are widespread in engineering systems and life sciences and play a key role in the understanding of these systems. In this paper, we develop a direct adaptive control framework for nonlinear uncertain nonnegative and compartmental dynamical systems. The proposed framework is Lyapunov-based and guarantees partial asymptotic set-point regulation; that is, asymptotic set-point regulation with respect to part of the closed-loop system states associated with the plant. In addition, the adaptive controller guarantees that the physical system states remain in the nonnegative orthant of the state space. (C) 2004 Elsevier Ltd. All rights reserved.