A chakra is an spinning energy center that manages the flow of life force energy (also called prana or chi) that gives life to our physical, mental, emotional and spiritual state.  They are energetic organs, not physical ones, so they cannot be detected by traditional medical equipment.  There are many chakras in the human energetic anatomy, but most focus on the 7 major chakras.

7 major chakras

Root chakraSacral chakraSolar Plexus chakraHeart chakraThroat chakra3rd eye chakraCrown chakra