Elevated homocysteine plasma concentrations are known as an independent risk indicator of cardiovascular and many other diseases. To assess if plasma homocysteine mirrors homocysteine concentrations in various tissues, we fed rats with either a normal (n = 9) or a methionine enriched (n = 9) diet for four weeks. Homocysteine and its precursors were determined in liver, heart, kidney, spleen, brain and plasma. To check for an influence of study conditions, further studies were performed with 1) 1 or 2 % homocysteine, 2) 1 % methionine supplementation, or 3) vitamine B12 and folic acid depletion for three months. In methionine-enriched fed rats, plasma homocysteine was two-fold elevated. Homocysteine tissue levels were elevated only in spleen (1.5-fold) and S-adenosyl-homocysteine (SAH) levels were elevated only in liver (1.5-fold). Feeding rats with methionine enriched diet for 3 months led to a stronger elevation in liver SAH (3-fold), whereas homocysteine enriched diet or vitamine depletion did not alter liver SAH concentrations. In conclusion, we found that alterations of homocysteine concentrations are highly tissue specific. Furthermore, alterations in homocysteine metabolism strongly depend on the conditions of study.