Why are my jalapenos turning brown? The plant looks healthy. The fruit turns brown after it is about inch and a half from tip to stem.
It may be blossom end rot, does it look like this: http://www.caes.uga.edu/applications/publications/files/html/C938/images/Figure7.jpg ?
If it is, blossom end rot is caused by a lack of calcium to the plant.
Have you had your soil tested? It might show that you need to increase the calcium in the soil. There are plenty of organic fertilizers that are aimed for tomatoes & vegetables that will contain calcium.
Have you been over fertilizing with high nitrogen fertilizers?
Are you watering enough? Water is needed to bring the calcium up through the roots.
You can check out this publication http://www.caes.uga.edu/publications/pubDetail.cfm?pk_id=7801 for more information.