The investigation of adverse health effects associated with fungal mycotoxins requires the measurement of human exposure. Most frequently, this exposure is estimated from contamination levels of raw foodstuffs, which are the primary source of toxin exposure, and data on food consumption patterns. However, variations in food preparation methods, food intake, contamination level, intestinal absorption, toxin distribution and excretion lead to individual variations in toxin exposure that are more readily measured with a biomarker. Fumonisin biomarkers have been sought in the measurement of levels of the toxin in physiological samples such as serum, urine, faeces, hair and nails. However, due to the low bioavailability of fumonisin, these samples pose a variety of analytical challenges and also still require validation as biomarkers. The most widely researched fumonisin biomarkers have been those related to the disruption of de novo sphingolipid biosynthesis, namely elevated levels of the sphingoid base, sphinganine, or of its ratio with sphingosine. Elevation of these parameters in humans would potentially provide a biomarker of biochemical effect. A number of investigations into the possible elevation of sphinganine (or its ratio with sphingosine) in human blood and urine have generally failed to correlate with estimates of fumonisin exposure. The sphingoid bases occur naturally in human blood and urine such that their levels have normal ranges, which can be influenced by dietary factors other than fumonisin ingestion. The lower exposures from human diets, as compared with doses in experimental animals, have made detection of changes in these sphingoid biomarkers problematic.