Fatty acid analysis is an important research tool, and indices derived from essential fatty acid contents serve as useful biomarkers related to cardiovascular and other chronic disease risk. Both clinical and basic studies of essential fatty acid composition are becoming ever larger in magnitude leading to delays while the rather laborious lipid analyses are performed. A robotic transesterification procedure has been developed for high-throughput analysis of plasma fatty acid methyl esters. In this approach, robots perform most steps including plasma and reagent transfer, transesterification reaction via heating at 80 °C in open tubes with multiple reagent additions, followed by two-phase extraction and transfer of lipid extracts to GC vials. The vials are then placed directly onto a GC autosampler carousel for robotic sample injection. An improved fast GC method is presented in which the peaks of interest are eluted within 6 min. This method is readily scalable to prepare and analyze 200 samples per day (1,000 samples per week) so that large clinical trials can be accommodated.