Columns made of three different materials were evaluated with regard to the carryover of phosphorylated peptides and fumonisins in liquid chromatography/tandem mass spectrometry (LC/MS/MS). In order to eliminate carryover caused by the injection operation in the autosampler, the column carryover was calculated using the duplicated solvent gradient method. A column made of a glass-lined stainless-steel tube and polyethylene frits (GL-PE column) yielded the most significant improvements in the peak shape and the carryover as compared to the other columns. The carryover of fumonisin B₁ (FB₁) and HLADLSpK (T19p) in the GL-PE column could be reduced; the lower limit of quantitation of T19p, and the range of the calibration curve were also improved. Since carryover peaks with the GL-PE column were symmetrical peaks of the samples, carryover in the column did not occur. The carryover calculated by the duplicated solvent gradient method corresponded to those in the flow path from the injection port to the inlet frit of the column. The carryover value of FB₁ in the column with a stainless-steel tube and stainless-steel frits (S-S column) was 1.70%, and that of the flow path was 0.23%. We found that the majority of the carryover in our system occurred in the S-S column.