Jalapeno Peppers contain capsaicin which is healthy for your body in moderation because the capsaicin can help fight off diseases such as cancer and boost your immune system so you may get the flu and cold virus less often as well.
But eating too many Jalapenos can eat at your stomach lining and even cause Ulcers to develop so if your stomach is starting to hurt as a result of eating Jalapenos then you're liking eating too many.
I don't Jalapeno Peppers everyday but when I do eat Jalapenos I never eat more than 4 Jalapenos in a day and although eating a few more is okay my stomach would start hurting bad if I ate more than 4 Jalapenos per day.