Introduction: Absorption of dietary fats is generally in the form of emulsions. The present study assessed the preparation and gastrointestinal absorption efficiency of three emulsions of mustard oil containing three types of medium chain fatty acids (MCFAs) in a rat model. Methods: Caprylic acid (C8:0), capric acid (C10:0) and lauric acid (C12:0) were chosen as the MCFAs. Mustard oil emulsions were formulated using each of the MCFAs and lecithin as an emulsifier. The characteristics of the formulations including optical microscopy, particle size, zeta potential analysis and viscosity studies were assessed. Thereafter the intestinal digestion patterns of the three MCFA rich mustard oil emulsions were compared using a single pass perfusion test. Results: The particle size of the emulsions varied between 212.70 nm and 312.70 nm. Physical characterisation such as a zeta potential study confirmed that all emulsions were thermodynamically stable. The absorption study was monitored at 30 min intervals of up to 2 h The absorption of C8:0 emulsion was found to be maximum (27.78%) followed by C10:0 emulsion (24.81%) and C12:0 emulsion (22.50%). The differences in absorption efficiency of the emulsions could be attributed to the smaller chain length of C8:0 which was more rapidly absorbed by the intestine. Conclusion: In vivo gastrointestinal absorption of MCFA rich mustard oil emulsions was compared; caprylic acid-rich mustard oil showed the highest absorption rate in comparison to the other two emulsions. Further in vivo studies are required to establish the mechanism of absorption of structured lipids containing MCFAs.