Three-dimensional water phantoms are routinely used when acquiring the data necessary to commission medical linear accelerators. A new water phantom controller has been developed at our institution that is unique in several aspects. The water phantom controller is based on an IBM XT compatible computer. This has been interfaced to an Artronix three-dimensional water phantom and a commercially available linac setup controller. Some of the unique features of the new controller are (i) its ability to perform three-dimensional coordinate transformations on the fly (this removes the need to level and align the water tank with the beam axes and greatly reduces setup time). (ii) Its ability to communicate with a device which can control the linac operating parameters (this allows the water phantom controller to adjust, for example, the jaw size of the accelerator as it acquires data). (iii) Its ability to output the acquired data in a number of modes, including screen display, hardcopy plot, or disk file that may be transferred to a central treatment planning computer). (iv) Its ability to digitally process the acquired data. This water phantom controller may be used to gather machine data in a highly automated manner, greatly reducing the time required to gather the desired data.