Prepping the Wood
It's in your best interests to put down a large drop cloth under the window. You may also want to tape painter's plastic around the window if you're planning on painting the inside of the window. Be sure to use blue painters tape and not masking tape as this can cause the paint to bleed through and masking tape can damage drywall and other delicate surfaces.
New all wood windows need to be cleaned and primed before you can begin working on them. A wood cleanser can be used, but basic soap and water work just as well. Never use a degreaser or other chemical cleaners on wood as it may cause the wood to permanently stain, warp or twist.
Sanding the wood is essential to the paint adhering to the all wood window successfully. When the woods surface is pitted and grooved with fine sandpaper, paint can easily bond with the wood fibers and actually become part of the wood. Without this bond, paint will eventually flake off a wood window. Be sure to use fine grit sandpaper and always sand with the wood grain. Be careful when sanding around the window pane as it can permanently scratch the glass if you're not careful. Wipe away the wood dust using a dry paintbrush or dust cloth.
Apply the Primer
For this part of the project, you'll need to have a small 2' latex paintbrush to get at the smaller parts of your all wood window. You'll also need a quality latex binding primer to coat the window and get it ready to accept your latex paint. Apply a very light coat onto the window. You'll want to avoid any runs because these can easily seal the window shut, leak into sensitive window parts and make a mess. You'll need to paint the entire window, so getting right up to the edge of the glass is imperative. Don't worry if you get a little paint on the glass, it will easily come off later with a razorblade. Let the primmer dry for at least four hours. Open and close the window every half hour or so to prevent it from sticking shut.
Apply the Paint
Once the primer is dry, you can begin painting the latex paint onto the primer coat. You'll need to paint the windows using a very light coat of paint to prevent any runs or drips. Once you have the first paint of coat complete, let it dry for at least two hours, and then apply a second and third coat as needed. Open and close the window every half hour to prevent the window from sticking shut. Once it's all dry, scrape away the excess paint from the window with a razor blade.