The side effects of the main active ingredient in Prilosec OTC, omeprazole, may include headache and abdominal pain, according to WebMD. Serious, more rare side effects may include an irregular heartbeat, muscle spasms or seizures while using this product. A serious allergic reaction is highly uncommon from this product.
Most people who use Prilosec OTC do not experience any serious side effects, according to WebMD. This medication is used to treat frequent heartburn that occurs for more than two days a week, difficulty swallowing and consistent coughing, according to Drugs.com. The medicine works by decreasing the amount of acid that is produced by the stomach.