This article represents the consideration of the issue of preventing prisoners from being ill-treated within the Council of Europe system for the protection of human rights. The reason for writing on this topic is that there have been some great changes in the protection of prisoners within the last 10 years. The biggest roles in creating better protection have been taken by the European Court of Human Rights (ECtHR) and the Committee for the Prevention of Torture (CPT). ECtHR has extended the interpretation of Article 3 of the European Convention for Human Rights (ECHR), while the CPT has generated some new standards that now directly influence the work of ECtHR. The Court had been reluctant to engage Article 3 to address the question of conditions of detention and preventive health care in prisons; it had always been focused on cases of deliberate ill-treatment by authorities towards detainees. The situation has changed within the last decade. The Court has drastically extended its interpretation of what constitutes violation of Article 3 and it is now relying on CPT reports when determining whether ill-treatment occurred. This new approach in the ECtHR’s jurisprudence now provides a potential tool to endorse some new rights under Article 3, like the right to needle exchange programmes for prisoners who inject drugs. On the other hand, the Court is overwhelmed with cases, the number of applications has been growing constantly during last years and it does not seem very likely that this problem will be solved in the near future. ECtHR needs an urgent reform to deal with the continuing increase in the number of applications. This was the main reason for drafting Protocol No. 14 which has been ratified by all Council of Europe member states but Russia. Russia thus constitutes the main holdback for reforming the Convention system and consequently strengthening the protection of prisoners. Protocol No. 14 is currently the only available solution to the Council of Europe in order to reduce the number of applications pending before ECtHR. At the same time the majority of cases before the Court are against Russia, and Russia still finds it very hard to comply with the human rights standards. The prosperity of the ECtHR and its role as the most effective human rights court are seriously jeopardised.