Monoacylglycerols and diacylglycerols are intermediate compounds in biodiesel which result from incomplete transesterification reaction during biodiesel production. Traces of free glycerine and partially reacted triacylglycerols are also found in biodiesel. These contaminants cause serious operational problems in engines, such as engine deposits, filter plugging, and emissions of hazardous gasses. Increased levels of these contaminants in biodiesel compromise quality which is vital for commercialisation of this product. In this work, levels of free glycerine and total glycerine in jatropha methyl ester (JME) and castor methyl ester (CME) were determined using gas chromatography (GC) equipment. Amounts of free and total glycerine in JME and CME were generally high compared to the ASTM D6751 and EN14214 recommended values. Free glycerine from JME was 0.1% wt compared to 0.02% wt (ASTM D6751) and 0.01% wt (EN14214) values whereas the total glycerine from JME was 2.96% wt compared to 0.24 %wt (ASTM D6751) and 0.21% wt (EN14214). These discrepancies could have resulted from insufficient purification of the product and incomplete conversion or due to the high temperature associated with GC analysis that might have caused pyrolysis or thermal degradation of certain lipid components. Castor methyl ester free glycerine was 0.14% wt while total glycerine was 13.21% wt. This can still be explained by the same reasons given for JME. Thermal decomposition of lipid components in a GC could have interfered with the summative mass closure calculations that were done to determine the total composition of the biomass.