Upon arrival in Madrid, I will be going directly from the airport to Chamartin station, where I may have a wait of an hour or more for a train to Burgos. I've been to Spain several times without incident, and I've had pleasant experiences riding the rails, but I've never used Chamartin station. Since I've been reading and hearing a lot lately about increased crime in Madrid, I'm a bit concerned. I am female, traveling solo, with a small suitcase and a backpack. Is the waiting area pretty secure? Any advice?

Thanks!

Chamartin station is fine especially during the day. Wait in the main common areas instead of the platforms though if it's night.

Leche

Have you thought about taking a bus? Continental-Auto busses serve Burgos from Avenida de America multimodal transportation center. You can get to the Avda de America on the Metro from Barajas w/just one change (Mar de Cristal). It's about a 2.5 hour bus ride.
BTW
Chamartin is much more 'user friendly' than Puerta de Atocha. If you do take the train, there's a little store on the west end (inside the station) where you can buy some snacks/beverages for the train.