Blood choline has been proposed as a predictor of acute coronary syndrome (ACS), however different testing procedures might affect the choline concentration because the lysophospholipase D activity of autotaxin (ATX) can convert lysophosphatidylcholine to lysophosphatidic acid (LPA) and choline in human blood. Although the influences of ATX on LPA levels are well known in vivo and in vitro, those on choline have not been elucidated. Therefore, we established suitable sampling conditions and evaluated the usefulness of plasma choline concentrations as a biomarker for ACS. Serum LPA and choline concentrations dramatically increased after incubation depending on the presence of ATX, while their concentrations in plasma under several conditions were differently modulated. Plasma choline levels in genetically modified mice and healthy human subjects, however, were not influenced by the ATX level in vivo, while the plasma LPA concentrations were associated with ATX. With strict sample preparation, the plasma choline levels did not increase, but actually decreased in ACS patients. Our study revealed that ATX increased the choline concentrations after blood sampling but was not correlated with the choline concentrations in vivo; therefore, strict sample preparation will be necessary to investigate the possible use of choline as a biomarker.