This paper presents a mathematical programming approach for medium term planning of biopharmaceutical manufacture under uncertainty. The proposed mathematical formulation constitutes a modification of an earlier deterministic model [Lakhdar, K., Zhou, Y.H., Savery, J., Titchener-Hooker, N.J., Papageorgiou L.G., 2005, Medium term planning of biopharmaceutical manufacture using mathematical programming. Biotechnol Prog, 21: 1478-1489] determining the optimal production plans for a biopharmaceutical manufacturing facility, whereby this work allows for uncertain fermentation titres. The overall problem is formulated as a two-stage, multiscenario, mixed integer linear programming (MILP) model. An iterative algorithm is then proposed to allow for the solution of larger instances of the resulting large-scale MILP problem. The applicability of the proposed solution approach is demonstrated via a number of illustrative examples and is found to compare favourably with the deterministic model and the full-space model. Crown Copyright (c) 2007 Published by Elsevier B.V. All rights reserved.