LOD stands for "logarithm of the odds." In genetics, the LOD score is a statistical estimate of whether two genes, or a gene and a disease gene, are likely to be located near each other on a chromosome and are therefore likely to be inherited. A LOD score of 3 or higher is generally understood to mean that two genes are located close to each other on the chromosome. In terms of significance, a LOD score of 3 means the odds are a thousand to one that the two genes are linked, and therefore inherited together.
LOD score is actually an acronym for "log of the odds," LOD. LOD score actually refers to a numerical result when estimating whether two genes, or a gene and a disease, are linked to one another. LOD scores are most often used to describe the data one gets out of family studies where you are looking at large families and an inheritance of traits or diseases within the families. So you can have the gene of interest unlinked to your disease and have a very low LOD score. In a family where the gene and a particular disease are segregating or being inherited together the odds of those being linked can actually be quite great and that would be a large LOD score. For example, in a pedigree to prove that a gene is linked to a condition we usually say that the LOD score has to be above 3. 3 is translated roughly into about 1,000-to-one odds that this gene really is linked to this disease as opposed to the alternative hypothesis which is unlinked. So therefore the higher the LOD score the more likely the two things you are following, usually a disease and a gene or a marker, actually are truly linked in the family.