Adverse effects
Adverse effects occurring in at least 1% of people include:
Central nervous system: headache (7%), dizziness (2%)
Respiratory: upper respiratory tract infection (2%), cough (1%)
Gastrointestinal: abdominal pain (5%), diarrhea (4%), nausea (4%), vomiting (3%), flatulence (3%), acid regurgitation (2%), constipation (2%)
Neuromuscular and skeletal: back pain (1%), weakness (1%)
Dermatologic: rash (2%)Other concerns related to adverse effects are:

Recurrence of Clostridium difficile associated diarrhea
Osteoporosis-related fractures
HypomagnesemiaConcern has been expressed regarding vitamin B12 and iron malabsorption, but effects seem to be insignificant, especially when supplement therapy is provided.Since their introduction, proton-pump inhibitors (PPIs, especially omeprazole) have also been associated with several cases of acute interstitial nephritis, an inflammation of the kidneys that often occurs as an adverse drug reaction. Long-term use
Long-term use of PPIs is strongly associated with the development of benign polyps from fundic glands (which is distinct from fundic gland polyposis); these polyps do not cause cancer and resolve when PPIs are discontinued. No association is seen between PPI use and cancer, but use of PPIs may mask gastric cancers or other serious gastric problems and physicians should be aware of this effect.There is a possible association between long term use and dementia which requires further study to confirm.A review article in U.S. Pharmacist in 2013 states that long-term use of PPIs is associated with decreased calcium absorption (causing increased risk of osteoporosis and fractures), decreased magnesium absorption (causing electrolyte disturbances), and increased risk of certain infections such as C. difficile and community-acquired pneumonia. They hypothesize that this is due to decreased stomach acid production.
Additionally, most sources recommend that after taking omeprazole, at least 30 minutes should be allowed to elapse before eating (at least 60 minutes for immediate-release omeprazole plus sodium bicarbonate products, such as Zegerid), though some sources say that with delayed-release forms of omeprazole, waiting before eating after taking the medication is not necessary.Omeprazole is completely metabolized by the cytochrome P450 system, mainly in the liver, by CYP2C19 and CYP3A4 isoenzymes. Identified metabolites are the sulfone, the sulfide, and hydroxy-omeprazole, which exert no significant effect on acid secretion. About 77% of an orally given dose is excreted as metabolites in the urine, and the remainder is found in the feces, primarily originating from bile secretion. Omeprazole has a half life of 0.5 to 1 hour. The pharmacological effects of omeprazole last longer as it is covalently bonded to proton pump on parietal cells to induce effects. Chemistry
Omeprazole contains a tricoordinated sulfinyl sulfur in a pyramidal structure and therefore can exist as either the (S)- or (R)-enantiomers. Omeprazole is a racemate, an equal mixture of the two. In the acidic conditions of the canaliculi of parietal cells, both enantiomers are converted to achiral products (sulfenic acid and sulfenamide configurations) which react with a cysteine group in H+/K+ ATPase, thereby inhibiting the ability of the parietal cells to produce gastric acid. AstraZeneca also developed esomeprazole (Nexium) which is a eutomer, purely the (S)-enantiomer, rather than a racemate like omeprazole.