You basically have two options. There are fairly expensive marker pens sold for this express purpose by quilt shops. In theory, they will stand the test of being used on a quilt, although in practice you get a few bad reports. Option #2 is to use a marker pen which is designed for children and is sold as being washable, including from fabric. These are a lot cheaper and getting fairly popular, although there isn't as much data with these as there is with the ones sold by quilt shops. Again, most people like them but you do get the odd horror story. I've just started playing around with the Crayola washable markers myself.

I've used Crayola washable markers three times and had no trouble, though I read too much and all 3 times I've gotten up in the middle of the night to wash the quilt, even before the binding was attached. I scrub it with SHOUT (the deoderant-stick kind) before putting it in the washer - maybe I don't need to, but it makes me feel more confident. They say DON"T USE THE YELLOW

Thanks for this info. I got those markers but haven't used them because some people here were saying they couldn't get the marks out. Now I'm going to try them. Thanks!!

Experiment with scrap fabric before you use them in a quilt. I tried going over each line about twenty times, pressing with a hot iron, and then slinging the sample piece in the wash. Most colours washed out entirely, a few left faint lines, and even those faded away. I'm still being cautious, but I reckon that if it can stand up to that, it can stand up to basic quilt marking.

I use these markers all the time. Once I Had the brown marks appear when I washed it when I finished it. Instead of putting in plain cold water FIRST to remove the marks, I just added it to the washer with soap and oxyclean! Big mistake! To remove the Brown marks, I had to soak the whole quilt in a mixture of white vinegar and water. Thankfully, the brown markings came off. Then I rinsed it in lots of clear water, the re-washed it with soap. Came out perfectly! Gave the quilt away and there have been no more problems. Thankfully!!!