In this work a diagnosis is presented for the elaboration of a manual of policies and procedures that offers an orientation for the execution of an audit program, that generates trustworthiness to the entities before the environmental impact product of the development of their business activities; It will be developed in three phases, where it will initially collect information related to the policies and procedures of an audit of the environmental management system (EMS) for the institutions that provide indigenous health services (IPSI), which recognizes a relevant documentary base for the study of the regulations that define the policies and procedures that link the Public Accountant as a notable piece in the EMS auditing processes, and establish the policies and procedures to develop an audit of the environmental management system in the IPSI that guarantees reliability before the impact of their activities on the environment.