It's important to remember that Flonase is a corticosteroid. This makes it a powerful medication, but there's also the possibility of side effects. For example, my doctor worried about prescribing Flonase for my allergy symptoms, because he was concerned it could raise my blood pressure. Even the Flonase web site lists several mild side effects which "may include headache, nosebleed, or sore throat." But if you read a little further down, you'll see the manufacturer warning you about a longer list of "other risks".
For example, corticosteroids "can slow the healing of wounds". This seems like it could be problematic in certain scenarios, and the manufacturer specifically warns about its possible effect on pre-existing injuries to the nose. ("Do not use Flonase until your nose has healed if you have a sore in your nose, if you have surgery on your nose, or if your nose has been injured.") Apparently a wound is also more likely to get infected if a patient is using Flonase, since the manufacturer specifically warns that "Immune system effects may increase the risk of infections." And in addition, some patients "may have eye problems, including glaucoma and cataracts," according to the manufacturer, which warn users to get regular eye exams to check for any possible eye symptoms.
Flonase also affects some people more than others. For example, the Flonase site warns that corticosteroids "may slow growth in children." (Their proposed solution? "A child taking Flonase should have his/her growth checked regularly...") They also warn that before taking Flonase, your doctor should know if you're pregnant (or expect to be pregant soon), or if you're breastfeeding a baby - presumably because there's also additional side effects.
But even if you don't fall into those categories, the drug may have other effects, according to one study by the FDA. They specifically focused on what happens when the drug is applied to the skin, but if I'm reading their results correctly, the same information could be applied to the Flonase nasal spray. The most commonly commonly reported effects - ranging from 2.6% to .6% of the patients - were itching and dryness, as well as a burning sensation and even some numbing.
But here's the most important thing to remember about side effects: you have to pay attention to your body to notice them! Even the Flonase web site warns you should contact your doctor if the Flonase leaves you "feeling unwell or have any symptoms that you do not understand". Often it's hard to make the connection between the feelings in your body and the medications that you're taking. That's why it's important to be aware of the possible side effects which have been reported. If you're aware of what your body feels like before you're taking a medication, this makes it easier for you to notice any changes that occur later!