Pepper spray is an inflammatory agent. It inflames the mucous membranes in the eyes, nose, throat and lungs.  It causes immediate closing of the eyes, difficulty breathing, runny nose, and coughing. The duration of its effects depends on the strength of the spray; the average full effect lasts from 20 to 90 minutes, but eye irritation and redness can last for up to 24 hours.
The Journal of Investigative Ophthalmology and Visual Science published a study that concluded that single exposure of the eye to OC is harmless, but repeated exposure can result in long-lasting changes in corneal sensitivity. They found no lasting decrease in visual acuity.
The European Parliament Scientific and Technological Options Assessment (STOA) published in 1998 "An Appraisal of Technologies of Political Control"
The STOA appraisal states:
::"Past experience has shown that to rely on manufacturers unsubstantiated claims about the absence of hazards is unwise. In the US, companies making crowd control weapons, (e.g. pepper-gas manufacturer Zarc International), have put their technical data in the public domain without loss of profitability."
:and
::"Research on chemical irritants should be published in open scientific journals before authorization for any usage is permitted and that the safety criteria for such chemicals should be treated as if they were drugs rather than riot control agents;"
For those taking drugs, or those subjected to restraining techniques that restrict the breathing passages, there is a risk of death. In 1995, the Los Angeles Times reported at least 61 deaths associated with police use of pepper spray since 1990 in the USA. The American Civil Liberties Union (ACLU) documented 27 people in police custody who died after exposure to pepper spray in California since 1993. However, the ACLU report counts all deaths occurring within hours of exposure to pepper spray regardless of prior interaction, taser use, or if drugs are involved. In all 27 cases listed by the ACLU, the coroners' report listed other factors as the primary cause of death; in a few cases the use of pepper spray may have been a contributing factor.
The US Army performed studies in 1993 at Aberdeen Proving Ground, and a UNC study in 2000 stated that the compound in peppers, capsaicin, is mildly mutagenic, and 10% of mice exposed to it developed cancer. Where the study also found many beneficial effects of capsaicin, the Occupational Safety and Health Administration released statements declaring exposure of employees to OC is an unnecessary health risk. As of 1999, it was in use by more than 2,000 public safety agencies.
The head of the FBIs Less-Than-Lethal Weapons Program at the time of the 1991 study, Special Agent Thomas W. W. Ward, was fired by the FBI and was sentenced to two months in prison for receiving payments from a pepper-gas manufacturer while conducting and authoring the FBI study that eventually approved pepper spray for FBI use.  Prosecutors said that from December 1989 through 1990, Ward received about $5,000 a month for a total of $57,500, from Luckey Police Products, a Fort Lauderdale, Florida-based company that was a major producer and supplier of pepper spray. The payments were paid through a Florida company owned by Wards wife.
Direct close-range spray can cause more serious eye irritation by attacking the cornea with a concentrated stream of liquid (the so-called "hydraulic needle" effect). Some brands have addressed this problem by means of an elliptically cone-shaped spray pattern.
Pepper spray has been associated with positional asphyxiation of individuals in police custody. There is much debate over the actual cause of death in these cases. There have been few controlled clinical studies of the human health effects of pepper spray marketed for police use, and those studies are contradictory. Some studies have found no harmful effects beyond the effects described above.  Due to these studies and deaths, many law enforcement agencies have moved to include policies and training to prevent positional deaths.  However, there are some scientific studies that argue the positional asphyxiation claim is a myth due to pinpoint pressure on a person. The study by two universities stressed that no pressure should be applied to the neck area. They concluded that the persons own weight is not scientifically enough to stop a persons breathing with the rest of their body supported.