A selective and sensitive method for the determination of free and total proline (Pro) and 4-hydroxyproline (Hyp) by gas chromatography (GC) was developed. For free Pro and Hyp analysis, plasma and tissue homogenate were extracted with methanol. For total Pro and Hyp analysis, these samples were hydrolysed in 6 M HCl. After removal of primary amino compounds by the reaction with o-phthaldialdehyde, Pro and Hyp in methanol extract and acid hydrolysate were converted into their N-dimethylthiophosphoryl methyl ester derivatives and then determined by GC with flame photometric detection using a DB-5 capillary column. This method was successfully applied to small samples without prior clean-up, and Pro and Hyp in these samples could be analysed without any influence from coexisting substances. Overall recoveries of Pro and Hyp added to plasma and tissue samples were 92-106%. The analytical results of free and total Pro and Hyp in human plasma and mouse tissue samples are presented.