The paper aims to investigate the relationship between strategy and structure in the high-technology enterprises. The study attempts to ascertain how chief executive officers perceive the impact of strategy on organizational structure, and likewise impact of structure on strategy, at two phases in the innovation process: the phase of innovation exploration; and the phase of innovation exploitation. The research was conducted in 61 high-technology companies based in Poland that operate either in Poland or in the global marketplace. The results show that, during the exploration of innovation, chief executive officers consider that the impact of organizational structure on strategy is stronger than the impact of strategy on structure. During the exploitation of innovations, the impact of strategy on structure is stronger.