The speciations of the heavy metals (Cu, Cd, Cr, Pb and Zn) in paddy soils under the rice-wheat rotation cultivation in Chengdu Plain were determined with the chemical fractionation method. The contents of heavy metals in seeds of both rice and wheat grown in these soils at the same sampling sites were also determined to estimate the bioavailability of these heavy metal fractions. Statistical analyses including correlation analysis and multiple linear regression revealed that concentrations of Cr, Cu, Pb, and Zn in all the paddy soils decreased in the following order: Residue＞Bound to Organic Matter＞Bound to Iron and Manganese Oxides＞Bound to Carbonates＞Exchangeable, while that for Cd decreased in a different order: Bound to Iron and Manganese Oxides＞Residue＞Bound to Carbonates＞Bound to Organic Matter＞Exchangeable. Regarding the labile fractions (sum of all fractions excluding the residue), the content of Cd is the highest, while that for Cr the lowest in those paddy soils. Except for Cr, the contents of the labile fractions of all the heavy metals studied were correlated with their total contents. This is especially true for Cd with the correlation between the total content of Cd and that of all fractions significant at a 99% confidence level. Significant correlations at 95% to 99% confidence levels were also found between the content of the fraction “Bound to Iron and Manganese Oxides” or “Bound to Organic Matter” and the total contents for Cu and Zn, and between the content of “Exchangeable” or “Bound to Iron and Manganese Oxides” fraction and the total content for Pb. Relative to the national standards on heavy metals in foods by the Chinese Ministry of Health, the contents of Cd, Cr, Cu and Pb in the wheat seeds exceed the upper limit by 14.71%、870%、6.50% and 17.40%, respectively. In the rice seeds, however, only the contents of Pb and Cd were over the upper limits (by 10.90% and 8.70%, respectively). The speciation of these heavy metals in the paddy soils apparently affected the accumulation of the different heavy metals in the seeds of wheat and rice, but the exact effect varied for different elements. For example, regarding the regression coefficients in these multiple linear regression equations, the content of Cd in seeds of both rice and wheat were positively related to the contents of all labile fractions of Cd except two fractions “Bound to Iron and Manganese Oxides” and “Bound to Organic Matter”, while a negative correlation was found between the Cd contents in seeds and these two fractions. The content of Cu in the seeds of rice and wheat was highly correlated to that of the Exchangeable Cu, but also related to that of the Cu fraction bound to carbonate as well. The correlation between the content of Pb in the seeds and any labile fractions was weak and no difference was found between the various fractions in this regard. Finally, there was no significant relationship between the content of Zn in the seeds and that of any fractions of Zn in the paddy soils.