Contamination of grains with mycotoxins results in a dietary background exposure of the general population. In occupational settings such as during processing of raw materials as in milling, an additional mycotoxin exposure by inhalation is possible. Biomonitoring is an integrative approach to assess human exposure from various sources and by all routes. To investigate possible workplace exposure to mycotoxins, a pilot study was conducted that compared levels of urinary biomarkers in mill workers to those in a control group with dietary mycotoxin intake alone. Workers (n = 17) from three grain mills in North Rhine Westphalia, Germany, provided spot urines during shift; volunteers (n = 13, IfADo staff) with matched age structure served as control group. The mycotoxins selected for biomarker analysis were citrinin (CIT) deoxynivalenol (DON), ochratoxin A (OTA), and zearalenone (ZEN). Immunoaffinity columns (CIT, DON, ZEN) or liquid-liquid extraction (OTA) was employed for urine sample cleanup prior to targeted analysis by liquid chromatography with tandem mass spectrometry (LC-MS/MS) or by high-performance liquid chromatography (HPLC). In addition, mycotoxin metabolites that may be formed in the organism were analyzed, including deepoxy-deoxynivalenol (DOM-1), ochratoxin alpha (OTalpha), dihydrocitrinone (DH-CIT), and alpha- and beta-zearalenol (alpha- and beta-ZEL), as well as phase II metabolites that were hydrolyzed with beta-glucuronidase/arylsulfatase prior to sample cleanup. All analyte concentrations were adjusted for creatinine (crea) content in the spot urine samples. Citrinin, DON, OTA, and ZEN were detected in nearly all urine samples from mill workers and controls. Interestingly, DH-CIT was found at higher mean levels than the parent compound (~0.14 and 0.045 g/g crea, respectively), suggesting an effective metabolism of CIT in humans. Other metabolites DOM-1, OTalpha, and alpha- and beta-ZEL were detected less frequently in urine. Deoxynivalenol was detected at the highest concentrations (mean ~6 g/g crea), followed by OTA (mean ~0.08 g/g crea); ZEN (mean ~0.03 g/g crea) and its metabolites appeared in urine at lower levels. Mycotoxin biomarker levels in urine from mill workers and controls were not significantly different. From these results it is concluded that biomarker levels measured in urine samples from the two cohorts reflect mainly dietary mycotoxin exposure. An additional occupational (inhalational) exposure of mill workers, if any, is apparently low at the investigated workplaces.