Background: Prostanoids are used in the treatment of Raynaud’s phenomenon and acral perfusion disorders secondary to collagenosis. In subjective terms, intravenous administration of these agents produces success in more than 50% of patients. The therapeutic outcome of clinical administration of alprostadil or iloprost may vary from individual to individual. Patients and methods: The following variables were analysed in a cross-over study in 27 patients with collagenosis and Raynaud’s phenomenon: plasma viscosity and erythrocyte aggregation (rheological variables), partial pressure of oxygen and laser Doppler flowmetry in the finger region, and lymphocyte phenotyping and interleukin (IL) determinations (immunological variables). Results: Laser Doppler flowmetry revealed significant differences between patients with secondary Raynaud’s phenomenon and a control group of 25 healthy subjects. Laser Doppler readings did not change significantly as a result of the treatments. Therapy with iloprost produced a reduction in IL-1beta, L-selectin (CD 62 L) and IL-6. Conclusion: The change in immunological variables due to iloprost may explain the long-term effects of prostaglandins in the treatment of Raynaud’s phenomenon. From our results it is not possible to infer any preference for iloprost or alprostadil.