In 2016 Albania went through a major justice reform which provided legislative changes to the already existing institutions, established new ones and sought to improve the procedural guarantees of the accused in criminal trials. While the Albanian Code of Criminal Procedure prior to the changes did not provide for biological evidence or a medical intervention in the course of a criminal investigation, the new legislative changes introduced the concepts of biological evidence and the compulsory physical examination as part of tools in search of the evidence. Even though the draft amendments to the previous Albanian Code of Criminal procedure recognized the problems encountered in practice during the collection of biological evidence vis à vis individual’s rights to personal integrity and dignity, the application of newly introduced and enacted provisions remains still unclear and raises concerns, not only regarding the possible arbitrary use of such tools by law enforcement authorities, but also on the possible conflicts that can arise from the application of such procedures by medical examiners and physicians and the fundamental rights of the person under examination or undergoing the medical procedure/intervention.