--Rose is quite accurate in mentioning the most common reasons for high homocysteine levels are inadequate levels of the B-vitamins. Homocysteine is an amino acid that is made as a byproduct of the methylation chemical process in the body, and itself needs to be further "processed" into usable amino acids; B-vitamins are a big part of that process. If too much homcysteine builds up, it can oxidize low density lipoproteins in cholesterol, making them much more likely to stick to arterial walls and narrowing them. It also tends to increase coagulation. This is why homocysteine levels are often monitored by cardiologists as an indicator of the likelihood of coronary artery disease.

Homocysteine and MMA levels measured together are a good (though not perfect) indicator of B12 deficiency--better than just a serum B12 level. One might also have an elevated homocysteine level with folate or B6 deficiences, and it also might be caused by certain medications, or by low thyroid horomone levels or kidney problems--have there been any indications of these in your dad?