Myotubularin‐related proteins are a large family of phosphatases that have the catalytic activity of dephosphorylating the phospholipid molecules phosphatidylinositol 3‐phosphate and phosphatidylinositol 3,5‐bisphosphate. Each of the 14 family members contains a phosphatase catalytic domain, which is inactive in six family members owing to amino‐acid changes in a key motif for the activity. All of the members also bear PH‐GRAM domains, which have low homologies between them and have roles that are not yet clear. Here, the cloning, expression, purification and crystallization of human myotubularin‐related protein 3 encompassing the PH‐GRAM and the phosphatase catalytic domain are reported. Preliminary X‐ray crystallographic analysis shows that the crystals diffracted to 3.30 Å resolution at a synchrotron X‐ray source. The crystals belonged to space group C2, with unit‐cell parameters a = 323.3, b = 263.3, c = 149.4 Å, β = 109.7°.