Design the layout of the bathroom you want to build. This can be done with graph paper purchased at your local craft store. If you are looking for computer images you can use free interactive bath design tools such as the one on HGTVBathDesign.com.
Shop for a new toilet, bathtub or shower and sink with a vanity. If you're searching for a custom look then you can build a vanity to your specifications. If matching pieces are necessary then purchase them all at the same time. This can insure you have an exact idea of how they will look together. Don't forget the new flooring. Linoleum or tile works great in a bathroom because of the added moisture.
Install the bathtub or shower first. This will likely be the largest object to get into the bathroom. Having it installed first allows for space to be evaluated before you continue to build the rest of the bathroom.
Place the toilet and install proper flanges. Be sure to check for possible leak sights. When the toilet is in place properly, seal the bottom of the base with caulking.
Add the vanity and sink to the bathroom. Be sure the plumbing is connected correctly to the sink before sealing it to the vanity. The vanity should be screwed to the wall for security. Add the doors and drawers if necessary.
Lay the floor. Linoleum can be cut to fit and glued to the plywood on the floor. If tiling, set pieces in place and cut the tiles to fit corners and along walls. Finish by adding the grout to secure the tiles together.
Paint the walls with your choice of color and place decorative textiles in the new bathroom. Fresh flowers add a nice touch when showing the new bathroom off to friends.