For toxicological studies of B-type fumonisin in animals, high amounts of pure fumonisins are needed. In the past, several methods for the isolation and purification of fumonisins have been published, stating the problem of high losses of fumonisins during chromatography on solid phases. In this manuscript we describe a new approach based on liquid-liquid partition techniques using centrifugal partition chromatography in combination with ion exchange chromatography for the large-scale isolation of B-type fumonisins with good recovery rates, minimizing losses of fumonisins during the purification. A batch of cultures grown on solid media of 2 kg maize yields approximately 1 g of pure fumonisins with a purity of >98%.