We describe an improved whole blood folate analysis method that facilitates increased throughput compared to our previous method (Dueker et al. (2000) Anal. Biochem. 283, 266). Improvements include three items: first, a buffered solvent exchange to remove interfering amino acids, especially phenylalanine whose esters may interfere with the analysis because their retention times on the gas chromatography are close to those of the para-aminobenzoic acid (pABA) isotopomers; second, substituting an NH2 solid phase extraction step for an HPLC step permits the batch parallel processing of samples; third, replacing trifluoroacetyl derivatives of ethyl-esterified pABA isotopomers with heptafluorobutyl derivatives, which are better resolved on the GC column. The method measures pABA, a stable degradation product of folate. This simplifies sample handling and purification. Relative standard deviations are typically 5% or less and a single operator can process samples in batches of 40. Results from our GCMS method correlate (R = 0.98) with the Lactobacillus casei assay for whole blood folate. The modifications will facilitate the development of high throughput methods for whole blood folate. Our method holds promise for epidemiological and clinical studies, where accurate whole blood folate concentrations are needed. Because it is internally standardized, interlaboratory variation should be minimal.