The crystal structure and charge density of hydrogen (2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate, C(5)H(9)N(4)O(3)P x H(2)O, have been determined by means of single-crystal X-ray diffraction. Diffraction data were collected at 105 K with Mo K alpha radiation to a resolution of sin theta/lambda = 1.08 A(-1). A four-circle diffractometer equipped with a CCD area detector was used to collect 50 161 reflections over 3 d. 6082 unique reflections with I > 3 sigma(I) were used in the multipole model to map the deformation electron density and gave the final statistical factors R(F) = 0.0329, wR(F) = 0.0235 and g.o.f. = 1.37. Structure determination revealed that two O atoms in the crystal structure of the title compound act as hydrogen-bond acceptors for more than one hydrogen bond. Examination of deformation electron density maps showed preferential polarization of the lone-pair electron density of the two O atoms into the shortest hydrogen bonds.