Gout is another cause of swelling in the thumb. Many people think that gout only affects the toes, especially the big toe. But it also can affect the fingers and even joints like the knees. My grandfather used to have thumb gout. When a gout attack occurred, his thumb used to be very swollen and painful. It's caused by the build-up of uric acid crystals in the body. It's a very bothersome and uncomfortable condition.