We investigated different means of achieving methyl depletion by feeding weanling rats modified AIN diets depleted of folate (FD), folate + choline (FCD), and folate + choline + methionine (FCMD), and examined the consequent effects on folate status, homocysteine levels, and methylation status. Control rats were fed a 12% protein diet consisting of either casein or soy protein isolate (SPI) and containing 2 mg/kg folate, 0.2% choline, and 0.4% methionine. After the rats had been on the diets for 4 and 8 weeks, whole blood folate concentration was measured and found to be significantly depleted in the folate deficient treatments compared with controls at 4 weeks (p < 0.001), this reduction being significantly greater (p < 0.03) in casein-fed rats (60%) than in SPI-fed rats (32%). The omission of choline and methionine from the diet had no further influence on whole blood folate. A significant inverse correlation was observed in the casein-fed rats after 8 weeks between mean plasma homocysteine concentration and decreasing methyl content of the diet (r2 = 0.978, p < 0.002), an effect not seen in the corresponding SPI-fed rats. Hypomethylation of hepatic DNA evidenced by a reduction in 5-methylcytosine content was present in the casein rats fed FCD and FCMD relative to control (p < 0.05). No hepatic DNA methylation changes were observed in the SPI-fed rats. The results obtained in the present work demonstrate that a soy-based diet can compensate against methyl group depletion by maintaining plasma homocysteine levels and an adequate level of DNA methylation, a result we attribute to endogenous folate content.