Bovine pancreatic prophospholipase A2, the precursor of the lipolytic enzyme phospholipase A2, crystallizes in space group P3121 with cell dimensions a = b = 46.95, c = 102.0 Å. The structure was determined at 3.0 Å resolution using rotation and translation functions with transaminated phospholipase A2 as the model structure. The rotation-function calculations appeared to be sensitive to the resolution range selected. The results of the translation function were very well defined. Positioning of the model molecule according to the rotation- and translation-function results yielded an R factor of 0.44 for 2697 reflections between 7.1 and 3.0 Å. This could be decreased to 0.40 by a rigid-body R-factor search. Subsequent restrained refinement gave R = 0.27. The position of the calcium ion, which was excluded from the structure factor calculations, shows up as one of the highest features in difference Fourier syntheses. From the difference maps it also appears that the ten N-terminal residues of prophospholipase A2 are disordered. Disorder is also observed in the loop consisting of residues 62 to 73. This is quite in contrast to the situation in phospholipase A2 where this loop is well defined. The observed disorder may account for the large difference in activity of phospholipase and prophospholipase with respect to aggregated substrates like micelles.