During the implementation of eHealth projects, security is one of the key challenges. Security covers wide area, whether it is to ensure protection of the medical records, high availability of services, non repudiation of carried out activities, business continuity planning and many others. Therefore in Slovak national eHealth project (eSO1), security is implemented in depth and across the whole life cycle of solution development in order to ensure a high level of confidentiality, integrity and availability of data and services. The presentation deals with approaches and overview of security activities within the project eSO1.