This question pops up sometimes from tourists, especially those from foreign countries. Since there are hundreds of temples and shrines in Kyoto, I thought it would be a good idea to explain the differences between temples and shrines.
First of all, temples and shrines are totally different except for the fact that they are both related to religion; temples relate to Buddhism and shrines relate to Shintoism (I’ll give you a brief explanation about Shintoism later).
Temples have Buddha statues and priests/monks. When you visit a temple, you can actually see the Buddha statue while praying. This is one of the differences, because you can not see the object of worship in the shrine while praying.
Shrines usually exist for worshiping Kamisama (Japanese Gods). These are usually people or natural objects such as mountains. Shrines conduct ceremonies of Shintoism. Shinto does not have a specific origin. It was a way for worshiping nature and ancestors. It has developed through being affected by other religions such as Buddhism, which made it difficult to separate the two from one another.
Another big difference is that shrines have a gate called Torii whereas temples don’t. Torii gates exist to separate God’s area and people’s world, and when the Gods come down, they go through the gates. So it is advised not to go through the center of Torii gates, because that’s the route Gods use.
Also, the way you pray is different. At temples, if there is a place with water, wash your hands and rinse your mouth. Then bow in front of the coin box. If there is a bell, ring the bell with big wooden bar. Clasp your hands in front of your chest and pray. After praying, bow one more time. As for the way to pray in shrines, be sure to check the article “How to pray in shrines“.
You can find much more useful and complete information in my Kyoto Guidebook which is now available on Amazon sites. Click here to buy the Kyoto Guidebook (ebook) on Amazon.com (You can find the Kyoto Guidebook on your local Amazon site).