An automated protocol for the direct, rapid determination of isolated trans content of neat fats and oils by Fourier transform infrared (FTIR) spectroscopy was devised, based on a simple modification of the standard AOCS trans method, eliminating the use of CS 2 and methylation of low trans samples. Through the use of a commercially available, heated transmission flow cell, designed specifically for the analysis of neat fats and oils, a calibration (0-50%) was devised with trielaidin spiked into a certified, trans-free soybean oil. The single-beam spectra of the calibration standards were ratioed against the single-beam spectrum of the base oil, eliminating the spectral interference caused by underlying triglyceride absorptions, facilitating direct peak height measurements as per the AOCS IR trans method. The spectrometer was preprogrammed in Visual Basic to carry out all spectral manipulations, measurements, and calculations to produce trans results directly as well as to provide the operator with a simple interface to work from. The derived calibration was incorporated into the software package, obviating the need for further calibration because the program includes an automatic recalibration/standardization routine that automatically compensates for differences in optical characteristics between instruments, instrument drift over time, and cell wear. The modified AOCS FTIR analytical package was evaluated with Smalley check samples for repeatability, reproducibility, and accuracy, producing SD of ± 0.07, 0.13, and 0.70 trans, respectively, the FTIR predictions being linearly related to the Smalley means (r = 0.999; SD = ± 0.46), and well within one SD of the Smalley sample means. Calibration transfer was assessed by implementing the calibration on a second instrument and reanalyzing the Smalley check samples in cells of two different pathlengths (25-and 50-µm). There were no statistically significant differences between the FTIR trans predictions obtained for the Smalley samples from the two instruments and two cells, indicating that the software was able to adjust the calibrations to compensate for differences in instrument response and cell pathlength. The FTIR isolated trans analysis protocol developed by the McGill IR Group has the benefit of being based on the principles of an AOCS-approved method, matches its accuracy, and allows the analysis to be performed on both neat fats and oils, producing trans predictions in less than 2 min per sample. It is suggested that this integrated approach to trans analysis, which requires a minimum level of sample manipulation and operator skill, be considered as a modification of the proposed Recommended Practice CD14b-95. JAOCS 74, 907-913 (1997).Edible fats and oils vary in their triglyceride makeup, relative degree and forms of unsaturation (cis and trans), weight-average molecular weight, and overall fatty acid composition/distribution, and these complex determinants define the physicochemical properties of the lipid system. For stability and functionality reasons,...