Abstract Background and methods Workpackage 4 of EuroCareCF brought together a group of small and middle-size companies (SMEs) with strong interest in drug development for cystic fibrosis (CF). The common interest of SMEs and patient organizations (PO) in mutually beneficial cooperation was assessed. This was achieved by identifying critical unmet medical needs of CF patients and by analyzing fields of cooperation between SMEs and POs. Results Over and above all, finding a cure for the disease is considered the most important unmet medical need by POs. However, preventing or slowing down any further deterioration of health and the alleviation of symptoms are also considered valuable objectives. Areas of co-operation with SMEs include the preparation and conduct of clinical trials and co-operation in the post-marketing authorization period. Conclusions If a policy of transparency and respect for the independence of POs is applied, SMEs and POs can develop mutually beneficial and sustainable co-operation.