Chromosomes contain many genes, and since you have two copies of each chromosome (one from mom, one from dad), you also generally have two copies of each gene. Each copy is referred to as an allele. The alleles could be the same, or they could be different; it all depends on what you inherited from your parents. Which alleles you have inherited play a role in how the gene is expressed.
The sex chromosomes (X and Y) are obvious exceptions to this rule. Males only have one copy of X and one of Y; females do have two copies of X, but one of them is usually inactivated.
