A molecularly imprinted polymer (MIP) for the recognition of fumonisin B analogues (FB) using 2-(diethylamino) ethyl methacrylate (DEAEM) as functional monomer and trimethylolpropane trimethacrylate (TRIM) as cross-linker was prepared by bulk polymerization in acetonitrile. Fumonisin B(1) (FB(1)) was used as a template molecule. A molecularly imprinted solid-phase extraction (MISPE) procedure was developed for further application in the analysis of FB. The performance of the MIP throughout the clean-up of spiked bell pepper, rice and corn flake sample extracts was compared with the results obtained when using non-imprinted polymer, C(18), strong anion exchange and immunoaffinity sorbents. Extracts were analysed for FB with liquid chromatography-tandem mass spectrometry (LC-MS/MS) after clean-up. Depending on the food matrix and the concentration range of the fumonisins, recoveries after MISPE varied from 62 to 86%, from 62 to 83%, and from 67 to 81% for fumonisin B(1) (FB(1)), fumonisin B(2) (FB(2)) and fumonisin B(3) (FB(3)), respectively. The selectivity of the synthesized MIP for mycotoxins belonging to the group of FB was confirmed by evaluating cross-reactivity from analogue structures and other mycotoxins. Analysis of 39 naturally contaminated samples (corn flakes) by liquid chromatography tandem mass spectrometry indicated that the synthesized MIP could be an excellent alternative for clean-up and pre-concentration of FB in food samples. Pearson correlations between immunoaffinity clean-up and MISPE were calculated and amounted to 0.923 for FB(1), 0.808 for FB(2), and 0.759 for FB(3). It was shown that the developed MIP could be reused more than 50 times. The synthesis of an FB(1) imprinted polymer and its application in food analysis is reported for the first time.