second toe longer can lead to pain in the knees.  When it is longer than the big toe, it can put pressure on the joints in the foot and ankle, which can cause pain in the knees. The second toe being longer can also cause bunions, which are bony bumps that form on the joint at the base of the big toe. Bunions can be painful and can make it difficult to wear shoes. If your second toe is longer, you may want to see a doctor or podiatrist to find out if you need to have surgery to correct the problem. In most cases, it is not a serious condition and can be treated with stretching exercises and wearing comfortable shoes.