We compared several methods for producing haematin polymerisation at physiological temperatures (i.e., 37 degrees) and found that a trophozoite lysate-mediated reaction was inappropriate for measuring compound inhibition of haematin polymerisation. Using this method, we obtained significantly higher IC50 values (concentration inhibiting haematin polymerisation by 50%) for certain compounds than when other methods were used, including a food vacuole lysate-mediated reaction. This difference was probably due to the binding of these compounds to cytosolic parasite proteins, as proteinase K treatment of the trophozoite lysate reversed this effect. The initiation of haematin polymerisation was also investigated using several assays. It was found that haematin polymerisation occurred spontaneously, in the absence of preformed haemozoin, over a period of several days, but that the process was more rapid when an acetonitrile extract of malarial trophozoites was added. This extract contained no detectable protein, and its activity could be replicated using an extract from uninfected erythrocytes and by using lipids. We therefore postulate that no protein or parasite-specific material is absolutely required for the initiation of haematin polymerisation. The formation of beta-haematin de novo using the acetonitrile extract is more pH-dependent than the generation of newly synthesised beta-haematin from preformed haemozoin and cannot proceed much above pH = 6. We postulate that the initiation of haematin polymerisation is more sensitive to the equilibrium of haematin between its monomeric and mu-oxo dimer form and requires a higher concentration of monomer than for the elongation phase of polymerisation.