Two low phytic acid (lpa) rice mutant lines, Os-lpa-XS110-1 and Os-lpa-XS110-2, were grown together with their parent wild-type variety Xiushui 110 in four field trials. HPLC analysis of inositol phosphates in the seeds produced demonstrated that compared to the wild-type, the reduction in phytic acid content in Os-lpa-XS110-1 (-46%) was more pronounced than that in Os-lpa-XS110-2 (-23%). Lower inositol phosphates (InsP 3, InsP 4, InsP 5) were not detected in the mutants. The lpa mutants and the wild-type rice were subjected to comparative metabolite profiling by capillary gas chromatography. On average, 34% (Os-lpa-XS110-1) and 42% (Os-lpa-XS110-2) of the detected peaks were statistically significantly different between wild-type and mutants. However, only a few of these differences could be consistently observed for all field trials. Identification and quantification of the consistently different metabolites revealed that contents of myo-inositol and raffinose were increased in Os-lpa-XS110-1 but decreased in Os-lpa-XS110-2 compared to the wild-type. In addition, Os-lpa-XS110-1 exhibited increased levels of galactose and galactinol. Consideration of these metabolic changes in light of the routes involved in the biosynthesis of phytic acid indicated a disturbance in the early biosynthetic pathway of phytic acid in Os-lpa-XS110-2 (similar to the lpa-1 type mutation in maize) and a mutation event affecting phosphorylation of myo-inositol in Os-lpa-XS110-1 (similar to the lpa-3-type mutation).