My son is on Omnicef and woke up with hives this morning. How long will he break out with hives?

I wish I could give you an answer to your question. But if the hives are still coming out I would take my son to the ER immediately, as this (what you stated) is a serious side effect.

Serious Omnicef Side Effects
Some Omnicef side effects can indicate a potentially serious problem. If you experience any of these side effects, stop taking Omnicef and call your healthcare provider. These side effects include but are not limited to:

• Blood in stools
• Severe or watery diarrhea
• Unusual headaches
• Blurred vision
• Unexplained rash
• Itchy skin
• Hives
• Wheezing
• Difficulty breathing
• Swelling of the throat
• Peeling of the skin.

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Rare Side Effects
Rare side effects occur in less than 1 percent of people taking the drug. Because these side effects are so uncommon, it is difficult to tell whether they are actually caused by the medication or by something else.

Some of these rare side effects of Omnicef include but are not limited to:

• Serious allergic reaction
• Indigestion
• Bloody diarrhea
• Loss of appetite (anorexia)
• Heart failure
• Gas
• Inflammation of the vagina (vaginitis)
• Chest pain
• Constipation
• High blood pressure (hypertension)
• Increased rate of red blood cell destruction (hemolytic anemia)
• Reduced amount of platelets in the blood (thrombocytopenia)
• Liver failure
• Kidney failure
• Serious intestinal infection (enterocolitis).

http://www.drugs.com/sfx/omnicef-side-effects.html