Like all other chilli peppers, Jalapenos contain capsaicin. Capsaicin produces a sensation of heat or burning when it comes in contact with any skin tissue. So although this may increase flavour in your food, it is a definite horror when it comes in contact with your hands. Considering that the maximum amount of its heat is concentrated in the veins surrounding the seeds, deseeding and cutting jalapenos can be quite a problem.
The first thing that you should do is immerse your hands in a bowl of fresh lemon juice. If you do not have lemon juice, orange juice will do. Lemon juice is acidic and will help to break down the capsaicin oils that have been absorbed by your skin. You can use a detergent as well, although this will cause your skin to become dry and rough. After that, soak your hands in yogurt or milk for at least 20 minutes or so. This will help to neutralise the burning and will ease the burning sensation. Unfortunately this will only lessen the pain and not eliminate it completely. You can then make a thick paste out of baking soda and water and smear it over your hands. Allow your hands to dry completely before washing them with cold water. In all probability, your hands will now be completely fine (just a little sore with all the washing and scrubbing).
It seems that capsaicin affects different people differently. While some complain of a warm sensation other can be affected for days by the burning sensation. In rare cases, people actually get burn marks. The point that I must stress is that it is important to treat this problem as soon as possible so that you can reduce its effects. In future, I think that it would be wise to use latex or vinyl gloves when cutting jalapenos.
answered by G R