The average costs of data leakage are steadily on the rise. Especially in healthcare, the disclosure of sensitive information may have unfavorable consequences for the patient. As a consequence, several data security and access control mechanisms have been introduced, ranging from data encryption to intrusion detection or role-based access control, doing a great work in protecting sensitive information. However, the majority of these concepts are centrally controlled by administrators who are a major threat to the patients´ privacy. Apart from administrators, other internal persons, such as hospital staff members, may exploit their access rights to snoop around in private health data. This work presents PERiMETER, a security protocol for data privacy that is strictly controlled by the data owner. It integrates pseudonymization and encryption to create a methodology that uses pseudonyms as access control mechanism, protects secret cryptographic keys by a layer-based security model, and provides privacy-preserving querying.