Health organizations are increasingly investing in the implementation of quality management systems. Although there are a number of difficulties in assessing quality in health care, there is unanimity among managers that appropriate evaluation systems and indicators need to be chosen to support the administration of services and to provide more effective and efficient decision-making. When a service or product fails to meet any demand, a nonconformity is configured. Some companies often do not know how to create or implement a nonconformity management methodology or take action against any existing ones. Therefore, the general objective of this article is to propose a methodology of registration and treatment of nonconformity for medical diagnostic services by image. It is a qualitative-quantitative research of applied nature in the mode of technological production that counted on 12 participants experts. For such, the research was conducted from two main stages. The methodology created requires the support of a professional in the area of Information Technology, definition of processes and responsibilities in the company and also a work of dissemination and training to avoid resistance of employees. The methodology made it possible to generate on-line nonconformities, follow e-mail records and reminders, apply cause analysis, action plan and even record the effectiveness check, as well as interact with the employee at any time, attach documents and manage - via the report, taking into account the standard of the Program of Accreditation in Diagnosis by Image of the Brazilian College of Radiology. It is concluded that the methodology created helps to systematize the process of registration and treatment of nonconformities which contributes to the reduction of costs, feeding of internal indicators and evidence the importance of processes that are often not built or implemented for lack of knowledge or time.