Escalating intensity of rice cultivation has increased the burden on to the land in Indonesia through massive additions of chemical fertilizers and pesticides. To examine the long-term effects of intensive rice cultivation on the heavy metal content in sawah soil, a comparative study was conducted in Java, Indonesia. The term sawah refers to leveled and bounded rice fields with inlets and outlets for irrigation and drainage. Soil samples collected in 1970 and new samples from the same sites or close to the original sites were analyzed and compared. For the 40 sites studied, the topsoil layer had increased mean levels of several extractable heavy metals. Lead (Pb) increased from 6.02 to 8.67ppm (65.5%), boron (B) from 5.92 to 7.01ppm (18.5%), cadmium (Cd) from 1.00 to 1.41ppm (42.1%), cobalt (Co) from 1.82 to 2.24ppm (28.6%), copper (Cu) from 7.51 to 8.57ppm (18.0%), manganese (Mn) from 122.10 to 133.24ppm (9.8%) and zinc (Zn) from 5.64 to 7.58ppm (39.5%). The change in the average content of these heavy metals throughout the soil profile was smaller than that in the topsoil layer. Iron (Fe) was the only parameter that decreased over the study period. In the topsoil layer, Fe decline from 175.54 to 149.05ppm (14.0%), while throughout the soil profile it decreased from 158.89 to 96.44ppm (9.9%). The changes in extractable heavy metal content are strongly related to chemical fertilizer application and the increase in cultivation intensity. The initial content for all heavy metals examined was higher at seedfarm sites than at non-seedfarm site, because rice was planted at a higher cultivation index and chemical fertilizers were applied according to government recommendations at seedfarm sites. At non-seedfarm sites, on the other hand, rice and upland crops were planted in various rotation patterns with regular use of manure and low doses of chemical fertilizers. In 2003, both sites had equal cultivation indexes; thus, the changes in cultivation intensity at non-seedfarms were greater than at seedfarms over the study period. This resulted in a similar percentage change in the heavy metal content in this soil. Over the study period, the Pb content at seedfarms and non-seedfarms changed by 50.6% and 80.7%, respectively, while changes at seedfarm and non-seedfarm sites for other heavy metals were 20.1% and 17.3% for B; 43.4% and 42.7% for Cd; 27.0% and 22.9% for Co; 17.3% and 18.0% for Cu; -13.8% and 14.0% for Fe; 11.3% and 9.1% for Mn and 27.2% and 47.0% for Zn, respectively. The application of manure might be the main contributor to the large gap between the changes in Pb and Zn content at seedfarm and non-seedfarm sites.