The use of herbal supplements and medicines is rapidly growing as most people consider them as being of natural origin and therefore being safe. However, a significant number of patients combine herbal remedies with prescription medications and there is a growing evidence for interactions of drugs with herbal remedies or single compounds originating from plants. Beside metabolic interactions particularly on the level of barrier tissues being equipped with a multitude of transport proteins such interactions are reason of rising concern. One barrier of particular interest is the blood brain barrier separating blood circulation and central nervous system and protecting the brain from potentially toxic metabolites and xenobiotics. The present review gives a condensed overview about structure and function of the blood-brain barrier and interactions of selected compounds originating from natural products with transport proteins in the barrier.