This study probes in to the relationship between organization structure and perceptions of innovation in the pharmaceutical sector of India. Structure includes formalization, centralization, concentration of authority and participation in decision making. Innovation is measured by perceived innovation, that is, the perception of innovation in the organization. Data was collected using questionnaires and interviews. Results were analyzed using both quantitative (statistical) and qualitative (content analysis) techniques. Positive relationship was found between participation in decision making and perceived innovation. Negative relationship was found between centralization and perceived innovation, and between concentration of authority and perceived innovation. No significant relationship was found between formalization and perceived innovation.