The class B non-specific acid phosphatase AphA from Escherichia coli has been expressed in E. coli and purified following a new protocol. ESI mass spectroscopy shows that the purified enzyme solution contains two polypeptides with molecular weights differing by 185 Da corresponding to two different cleavage sites of the signal peptide from the AphA E. coli precursor. Despite the solution heterogeneity, X-ray quality crystals have been obtained. However, the crystals have a tendency to give polymorphs and to lose long-range order with time while maintaining an intact crystal habit. Crystals have been grown in space groups I222 and C2 with three different unit cells and different asymmetric unit contents. Diffraction data to 1.6 A resolution have been collected with synchrotron radiation at ESRF and DESY.