The killing of individual cells exposed to ionizing radiation has, in historic terms, been considered to be a consequence of direct hits by the radiation, but recent research has shown that cells in populations do not have to be directly exposed to radiation in order to suffer damage. In irradiated cell populations, this ‘bystander’ effect can be mediated by long-range transmission of toxic molecules or by direct transfer of molecules between cells. An important dynamic cellular process that controls the spread of the toxic effects of damage through a cell population is gap junction intercellular communication (GJIC). A critical limitation in the study of this phenomenon in irradiated cell populations is the lack of experimental systems that enable examination of the incidence of intercellular transmission of toxic effects, without clouding the definition of the mechanism by which it occurs. For instance, if high-energy radiation is used, the dispersal of the tracks means that interaction of the radiation cannot be confined to a single cell, which is in contact with other cells. This means that gap junction intercellular communication cannot be defined or studied under these circumstances. We describe the development and application of a laser plasma generated soft X-ray source, along with micro-masks manufactured by laser machining techniques, for the study of gap junction intercellular communication between adjacent, irradiated and nonirradiated cells.