There are some negative effects, yes.
Your body produces melatonin, which is a very efficient and powerful natural antioxidant, when you're in complete darkness. People who stay up all night are almost never in complete darkness and even a small amount of light will drastically reduce the amount of melatonin produced.
Your body is naturally programmed to be most active during the day, even if you are a night person. Just like not enough dark can mess with chemicals in your body, not enough light can too. Bright light, the kind that comes from the sun, is a natural stimulant and elevates the mood and metabolism. Artificial indoor light doesn't have nearly the same effect.
So basically, your body doesn't go through the normal circadian rhythm as well when you're a night person, because you don't experience the extremes of light and darkness that regulate that rhythm. Long-term effects can include depression, anxiety, weight gain, difficulty focusing, and a whole host of sleep disorders. Very long-term effects can cause elevated risk for heart and circulatory diseases and some types of cancer, weakened immune function, and early onset of problems associated with aging.
