Currently the adequate management of rare diseases and the rational use of orphan drugs constitute one of the most important challenges for the health system, furthermore these constitute a continuous challenge for Hospital Pharmacy Services. Rare diseases and orphan drugs management have high level of uncertainty due to small number of orphan drugs available, limited evidence on their benefit-risk ratio, and orphan drugs high price. The Hospital Pharmacy works to reduce the degree of uncertainty associated with the rare diseases pharmacotherapeutic management. To reach this goal is necessary to work on all the stages that constitute the pharmacotherapeutic process and that facilitate treatments availability, avoid inequalities, and achieve the best health results, and finally to contribute to health system sustainability . The work of the hospital pharmacist has been key in multiple stages of pharmacotherapeutic process such as evaluation, selection and planning of orphan drugs, acquisition and pharmacoeconomic management of orphan drugs, preparation of treatments, dispensing of medicines, monitoring and optimization of treatments by application of clinical pharmacokinetics or, more recently, approach humanization healthcare practices in patients with rare diseases.