95% or more of the old Japanese swords for sale on eBay today, were made tomorrow in China. Of the rest, many if not most have problems that the seller either doesn't know about or doesn't want to tell you about. The very few real and good quality Japanese swords on eBay are either labeled as such (maybe they have papers from one of the organizations in Japan) or they are diamonds in the rough. In the first case you will get a real and good quality sword but you'll most likely pay more than you'd have paid buying the same sword from a dealer; prices on eBay can be silly high. As for finding the diamond in the rough, the great sword for pennies on the dollar, even with decades of experience, can't always be identified from a few grainy pictures and a brief description. And if you can, then note that there are hundreds of fellow Nihonto enthusiasts who will have seen the same auction, and will bid at the end, driving the price up. There are few real bargains, and even fewer that slip through the cracks without everyone seeing them. Buying Japanese swords on eBay is a great way to burn through a pile of money fast. If you are a beginner you'd be smart to stay away from Nihonto on eBay.
Buying online, however, can be a great experience. Stick with well established dealers (many of which are linked on this Message Board) and ask advice if you're not sure about who is well esablished. Take your time, ask questions of the dealers, and study as much as possible about the sword you're considering.
Before even starting your search, read everything you can get your hands on, go to Japanese sword shows if possible, ask your way in to see other collector's collections, in short: STUDY. The more you know before you buy a sword, the better you'll do and the more you'll learn from the experience.