The performance of five different C18 chromatography analytical columns with different lengths, particle sizes and porosities were compared for analysis of ochratoxin A (OTA) in fungal cultures and raisin samples. Chromatographic parameters including retention time, limit of detection, limit of quantification, number of theoretical plates and reduced plate height were obtained and compared. This showed that, compared with traditional columns, shorter ones (100 and 75mm×4.6mm) with 2.7μm solid core particles are suitable for analysis of OTA in different matrices and allows a reduction of the total analysis time by approximately 50% without any detrimental effect on performance. This leads to significant reduction in analysis costs by savings in use of organic solvents and increasing the total number of analyses per day. The capability of these columns for analyzing samples, from different matrices, was assessed by analyzing OTA-contaminated samples from cultures of Aspergillus westerdijkiae and Aspergillus niger grown on a defined nutritional media (yeast extract sucrose agar) and from natural and OTA spiked raisins.