A pilot plant Fischer-Tropsch synthesis reaction was performed in a fixed bed reactor containing a precipitated iron catalyst. Sections were taken from the reactor and tested for Fischer-Tropsch activity in micro reactors. The catalyst sections were subjected to SEM, SIMS and XRD analysis and revealed catalyst deactivation due to (i) sulphur poisoning in the top portion of the reactor bed and (ii) magnetite formation and crystallite growth in the bottom portion of the reactor bed. (c) 2005 Elsevier B.V. All rights reserved.