Within the University of Basel, the European Center of Pharmaceutical Medicine or Institute of Pharmaceutical Medicine is embedded in the Department of Public Health (DPH) of the Medical Faculty and also has links with the Department of Clinical Research. The DPH regards a strong infrastructure for comparative effectiveness and health economic research as one requirement to position Basel as a primary player in health systems research with its high economic relevance.

Many of ECPM's research activities occur in cooperation with the following institutes/entities of the University of Basel:

• Basel Institute for Clinical Epidemiology & Biostatistics (CEB)
• Basel Pharmacoepidemiology Unit (BPU)
• Swiss Tropical and Public Health Institute (Swiss TPH)
• Institute of Nursing Science
• Faculty of Business and Economics (DHE), Chair of Health Economics

ECPM and the named institutes have identified the complementary strengths of each institution and a high potential for synergies and future collaboration. They have expertise in a number of closely related areas, implying large potential for economies of scale and scope. They have therefore joined forces to establish a network of excellence (S-CORE: Swiss Centre for Comparative Effectiveness and Health Economic Research). In early 2017, S-CORE has achieved formal recognition as a Research Network of the University of Basel.

Outside the University of Basel, the institute closely cooperates with the Epidemiology, Biostatistics and Prevention Institute of the University of Zurich and with the Department of General Internal Medicine, Inselspital, University of Bern and with the Clinical Trials Unit of the University of Bern. Since 2007, the Swiss Group for Clinical Cancer Research  (SAKK) and ECPM carry the SAKK Network Outcomes Research, with extensive activities in the areas of cancer-related outcomes research and health economics. Health Technology Assessment activities are performed within the framework of the Swiss Medical Board.
 
International cooperation occurs within project consortia performing European Union-funded projects, and within the Impact of Neutropenia in Chemotherapy-European Study Group.

Local academic collaborations

• Prof. Stefan Felder, Health Economics, Faculty of Business and Economics, University of Basel
• Basel Institute for Clinical Epidemiology and Biostatistics (ceb), University Hospital Basel
• Prof. Christoph Meier, Pharmacoepidemiology Unit, University of Basel, and Hospital Pharmacy Basel, University Hospital Basel
• Prof. Kurt Hersberger, Pharmaceutical Care Research Group, Faculty of Science, University of Basel
• Institute of Nursing Sciences, University of Basel
• Swiss Tropical and Public Health Institute
• Clinical units at University Hospital Basel

Collaborations with national and international academic and public entities

• Epidemiology, Biostatistics and Prevention Institute, University of Zurich
• University Hospital Zurich
• Institute of Social and Preventive Medicine, University of Bern
• Swiss Group for Clinical Cancer Research (SAKK)
• Swiss Federal Office of Public Health (BAG)
• INC-EU Study Group, Switzerland/UK

Collaborations with private entities

• Helsana Group Dübendorf, Switzerland
• Germany Breast Group, Neu-Isenburg, Germany
• Pharmaceutical companies