Deoxynivalenol is one of the most ubiquitous mycotoxins in the Western diet through its presence in cereals and cereal products. A vast amount of studies indicate the worrying level of exposure to this toxin, while even high percentages of the population exceed the tolerable daily intake. To evaluate and assess dietary exposure, analysis of urinary levels of deoxynivalenol and its glucuronides has been proposed as a reliable methodology. An indirect preliminary method was used based on the cleavage of deoxynivalenol glucuronides through the use of enzymes (β-glucuronidase) and subsequent determination of "total deoxynivalenol" (sum of free and released mycotoxins by hydrolysis). Next, a direct procedure for quantification of deoxynivalenol-3-glucuronide and deoxynivalenol-15-glucuronide was developed. As deoxynivalenol glucuronides reference standards are not commercially available, the indirect method is widely applied. However, to not underestimate the total deoxynivalenol exposure in urine, the direct and indirect methodologies need to be compared. Urinary samples (n = 96) with a confirmed presence of deoxynivalenol and/or deoxynivalenol glucuronides were analysed using both approaches. The indirect method clarified that not all deoxynivalenol glucuronides were transformed to free deoxynivalenol during enzymatic treatment, causing an underestimation of total deoxynivalenol. This short communication concludes on the application of direct or indirect assessment of urinary deoxynivalenol.