My child is 4 years old, and was on doxycycline bid for 7 days. what are the chances of his teeth staining? if so, will the only affect his baby teeth or his permanent teeth when they come in?

Firstly, all of his primary teeth are formed and erupted so they would not be affected. Doxycycline does not bind to calcium as well as older tetracycline medications did, so the research indicates there should be no issues. https://www.cdc.gov/rmsf/doxycycline/index.html

Doxycycline is the best treatment for rickettsial diseases such as Rocky Mountain Spotted Fever, which can cause considerably more morbidity than stained teeth. Tetracycline class drugs bind with calcium in forming permanent teeth and cause enamel irregularities including staining, but Doxycycline does not when used short-term, such as a week. Baby teeth are fully formed, so will not be affected.