New figures show the number of incidents has risen over the past three years, with tens of thousands of people affected.
A shocking catalogue of injuries and accidents has led to complaints that health boards are not doing enough to prevent problems occurring. Calls have also been made for a national approach to recording the incidents as Scotland's 14 health boards have differing policies.
The figures emerged after a Freedom of Information request from The Herald to Scotland's 14 health boards, as well as the National Waiting Times Centre, the Scottish Ambulance Service and the State Hospital at Carstairs to assess how many patients are suffering adverse effects unrelated to the reason they sought treatment.
More than half of the health boards reported a steady rise in the number of incidents and most said the number of extreme or major incidents was in the hundreds each year.
A major incident is defined as one in which a patient is seriously affected, for example due to a severe healthcare acquired infection (HAI) or a mistake where the wrong patient is treated or the wrong body part operated on.
An extreme incident includes those in which a patient dies unexpectedly or takes their own life, contracts a potentially fatal HAI, or is the victim of a homicide.
Health campaigner Rab Wilson, an ex-nurse who blew the whistle on a failure by NHS Ayrshire and Arran to publish serious incident reports, said: "Health boards haven't been learning from these incidents, but the health minister doesn't have the powers to hold health boards to account."
Mr Wilson's request for a copy of a report into a serious incident in which he was involved in February led to the disclosure of the circumstances surrounding 20 patients' deaths, which until then had been blocked on grounds of protecting confidentiality.
The more serious incidents in the documents involved three missed chances to diagnose cancers, the death of a patient trapped in a faulty lift, a death following inadequate treatment of a leg wound and two cases where psychiatric patients murdered or tried to murder a relative.
Ministers have ordered a probe to determine whether the health board had been intentionally trying to cover up the deaths.
NHS Greater Glasgow and Clyde said there were 150 extreme and 115 major incidents in 2009/10, rising to 154 extreme and 131 major in 2010/11, with 156 extreme and 156 major incidents in 2011/12.
NHS Lothian records the "actual harm" caused. In 2009/10 there were 200 causing "major" harm, and 73 deaths. The following year there were 131 incidents resulting in death and 141 classified as major, and last year 109 incidents resulting in death and 145 classed as "major".
One of the significant problems reflected is the lack of consistency in the way such incidents are recorded.
Ex-Health Secretary Nicola Sturgeon announced plans for new guidelines on dealing with serious incidents in the NHS in June. These are not yet in place.
The National Waiting Times Centre at the Golden Jubilee Hospital and the State Hospital were unable to separate incidents involving patients from those involving staff.
NHS Tayside gave the number of incidents and the categories it used to measure the degree of harm caused to patients, but claimed not to have a record of how many of the 7000 to 8000 incidents it records each year fell into any given category.
Many boards said the figures appeared high but should be seen in the context of the huge numbers of patients treated. NHS Greater Glasgow and Clyde said it served a population of 1.2 million and the board had handled in excess of 6.6 million attendances at surgeries and hospitals over the three-year period.
A spokesman said: "We encourage staff to report all incidents. This provides us with an opportunity to learn so that we can continue to improve the quality of patient care."
NHS Lothian said: "NHS Lothian treats 1.1 million patients per year. To demonstrate a positive safety culture we would want incident reporting to go up and harm to go down, as we have learned from the incidents."
Dr Jason Leitch, an ex-surgeon appointed by the Scottish Government to be the National Clinical Lead for Patient Safety, said Mr Wilson had exposed problems at NHS Ayrshire and Arran and he "had a point" about the need to learn from incidents.
However, he said he viewed rising numbers of recorded incidents as a good thing, as it represented a culture of reporting and learning from incidents.
He said recording could be more consistent, and that Healthcare Improvement Scotland will develop a national approach to measuring and learning from adverse events, with a consultation document due in January 2013.