A comparison has been made of an LC/MS/MS method using direct analysis of acetonitrile extracts of feed and cereal samples and a method using acetonitrile extraction and subsequent immunoaffinity column (IAC) cleanup. Naturally contaminated samples containing one or more of deoxynivalenol, zearalenone, T-2, and HT-2 toxins were analyzed together with test materials containing known toxin levels. LC/MS/MS ion ratios and peak profiles, repeatability, and LOQs were used as the basis for comparing the two approaches. The method without cleanup had poorer performance than the method with IAC cleanup in terms of identification based on ion ratios compared to standards. Without cleanup, there was more evidence of background interference, and monitored ions were invariably seen against a noisy background. Nevertheless, quantification of samples analyzed without cleanup gave reasonable agreement with the levels found in the same samples that had received IAC cleanup. Repeatability was poorer with no cleanup, and LOQ values were higher for HT-2 and 1-2 toxins, but there was no evidence of any adverse effects on MS performance with repeated injections of crude extracts. Overall, it was concluded that LC/MS/MS analysis of samples with no cleanup is adequate for screening, but for definitive measurements (e.g., for food regulatory control purposes) IAC cleanup remains essential.