Concentrations of deoxynivalenol (DON) and deepoxy deoxynivalenol (DOM-1) in animal blood are important parameters for studies in toxicology and biological detoxification of DON. Clean-up methods, using either immunoaffinity chromatography (IAC) or solid phase extraction (SPE), were compared in order to determine the free form of DON or DOM-1 and the sum amount (free form plus glucuronide conjugated form of DON or DOM-1), respectively, in swine serum. Detection was achieved by high performance liquid chromatography with ultraviolet detection (HPLC-UV). Compared with the SPE-HPLC method, the IAC-HPLC method provided lower quantitation limit (DON: 18 vs 42 ng/ml; DOM-1: 21 vs 30 ng/ml) and higher recoveries (DON: 93.4–102.7% vs 63.7–85.3%; DOM-1: 85.5–91.1% vs 68.0–82.6%). Compared with previously published methods, the developed IAC-HPLC method removed analytical interferences from swine serum in one quick and easy step, and eliminated steps of extraction with organic solvent and/or pre-purification using SPE cartridges. This IAC-HPLC method was used to analyze swine serum samples collected from pigs that were evaluated in a feeding trial of a microbiological detoxification of DON. No DON or DOM-1 were detected in serum samples from pigs given a toxin-free diet or a microbial control diet. In serum samples from pigs given a DON diet (5 mg/kg of DON), free form DON and sum free DON + conjugated DON were 38.8 ± 13.7 and 49.8 ± 14.1 ng/ml, respectively. In serum samples from those given a detoxified-DON diet (DON was transformed to DOM-1), free form DOM-1 was detected but not quantified, and the sum DOM-1 was found as 47.5 ± 6.3 ng/ml.