In biology a lot of technical terms are used, and sometimes because the words sound so strange it's easy to get confused. Personally when I was studying things like genetics and reproduction, I found that oftentimes I would have difficulty understanding concepts because I didn't really have a firm grasp of the little differences between things. For example, you will learn (if you haven't already) the terms gene, locus, allele, and chromosome. All of these deal with DNA, but they all refer to different things! One thing I've learned is that a good way to keep from getting confused is to really focus on understanding what each term means.

After reading your question, I think that maybe you are having this same problem! All the talk of chromosomes and homologous pairs can be very confusing, but if you really understand the difference between what each of these means you will find that it will be a lot easier to understand what happens during meiosis.

To get a better understanding of what chromosomes and homologous chromosome pairs are, let's first talk a little about shoes. Let's say that you have 26 shoes in your closet. Of course, not all of the shoes are totally different. If you take all of the shoes and match them up, you will find that while you have 26 shoes, you really only have 13 different types of shoe. Each type has a mate of the same type, forming 13 pairs of shoes. The 13 pairs are very different-- for example, one pair is made by Skechers and looks very sporty, while another pair is very smooth and dressy and made by Ralph Lauren. However, within each pair are two shoes that are basically the same design.

This is how the chromosomes in your cells are. You have 26 different chromosomes. However, just like with shoes, the chromosomes are arranged in pairs, meaning that you only have 13 different types of chromosomes. In order to distinguish between just general chromosomes and the specific similar chromosomes that match up to form a pair, the term "homologous chromosomes" is used. ("Homologous" can be thought of to just mean "the same type" in this case). Thus you have 13 different homologous chromosome pairs, with each pair made up of two homologous chromosomes. (In the shoe analogy, you have two different shoes by Skechers. The left shoe is one homologous shoe, and the right shoe is the other homologous shoe, together forming a homologous pair. These two shoes have to go together-- none of the other 24 remaining shoes match. They are just not homologous-- they aren't "the same type"! You would never wear one Skechers shoe and one Ralph Lauren shoe!)

If you match up all of the chromosomes in your cell into their proper pairs, they look different under the microscope, as you have observed. This is because they ARE different! Each different chromosome type carries different genes, and different numbers of genes. Therefore, in order to have all of the different genes, you need to have all of the different types of chromosomes! Happily, the way meiosis occurs guarantees that you will get all of the different types of chromosomes.

You inherited your chromosomes from your parents. Each of your parents gave you 13 chromosomes, so you have a total of 26. However, these chromosomes weren't just handed out haphazardly, or else you could be in trouble, because then you might not be lucky enough to get the right ones! Instead, to make sure that you get exactly the right chromosomes, the homologous pairs split apart during meiosis. (The homologous pairs do NOT stay together!) One half of each pair goes into one gamete, and the other half goes into another gamete. This way, each gamete has 13 chromosomes-- one of each different type. (So you see, the gametes do not contain any homologous pairs at all-- only one of each homologous chromosome). In this way, you get one of each type from your mom, and one of each type from your dad. When they come together, you have two of each type, making the proper total of 13 homologous chromosome pairs, with none of them (and the important genetic information they carry) being lost.

This question brings up a lot of interesting concepts about genetics. We have 23 pair of chromosomes. A picture of a person's chromosomes is called a karyotype. You can see one at this site:
human karyotype

Take a look at chromosome #1. This person inherited one copy of chromosome #1 from his dad and one from his mom. If you look at #3, the two chromosomes look different, but that's just because one was bending when the picture was taken. Now look at the last (23rd) pair, after #22. These two are really different. One is called an X chromosome, the other is a Y. That's how I knew this was a male. Females have 2 X chromosomes. The X chromosome has a lot of genes with a lot of information. The Y has about 9 working genes that basically tell the body to make this person male.

You might be wondering how a male gets by with fewer genes than a female. Most of the time it doesn't make a big difference in health. In fact, in each one of a female's cells, one X chromosome is 'switched off' and only one set of X genes is used. You could see this from a picture of my cat, Katie Lee. She's a "tortoiseshell" cat, meaning that she has splotches of black and orange. (Calico cats have more white, but also have black and orange patches.) What does this have to do with genes? The genes for both orange and black are dominant and on the X chromosome. If a cat gets a gene for black fur from one parent, and a gene for orange fur from the other, about half of her fur cells will make orange fur and half will make black fur, depending on which X chromosome is being used by that cell.

Why can't male cats be tortoiseshell or calico? Sometimes males have problems due to having only one X chromosome. If there is a "bad" gene on their only X, they don't have a chance of having a good copy. Females are less likely to have certain diseases or problems because if they have a bad gene on one X, they probably have a good copy on the other X.

Back to meiosis, remember that you have to divide the number of chromosomes in half (from 23 pair to 23) when making egg or sperm cells or the baby would have too many chromosomes. Each cell made by meiosis will have one complete set, but will be different because of the source of the genes. Chromosomes will be patchworks of the chromosomes inherited from the parents. But if all goes well, each one will look the same outside and have a complete set of genes.

For more on karyotypes, check out this site: karyotyping