In terms of official reports, the first identification of Minamata disease patients took place in 1956; hence, that year was marked as the year in which it occurred. Later studies led to a finding that a female child who developed symptoms in 1953 was patient number one.

Two sisters, aged 5 and 2, living in Minamata City, were the first patients who were officially reported in 1956.
They had dyskinesia and generalized convulsions as well as other symptoms, including dystonia of their hands and feet and sudden fits of screaming.
According to later studies, 17 out of 54 patients who were identified in that year had already deceased by the time.
There is a study report indicating the possibility that the disease had already occurred by 1942.

It was caused by methylmercury that had been accumulated in fish and shellfish after being discharged from the chemical factory into the sea.

Effluent discharged from the Minamata factory of Shin-Nippon Chisso Hiryo K.K. (now JNC Corporation) into the Yatsushiro Sea polluted the ocean, which caused methylmercury contained in the effluent to be passed on through the food chain to fish and shellfish living there, accumulating in high levels.
As the fish so contaminated with methylmercury did not look different from normal fish, people did eat them, and symptoms of Minamata disease appeared in those who had eaten a lot of them. Methylmercury, bound with a type of amino acid called cysteine, has a property of getting easily absorbed from the digestive tract and then penetrating into various parts of the body. Therefore, it can also make its way inside the brain and damage nerve cells, or cross the barrier of the placenta that connects a fetus with its mother, eventually entering the body of the fetus as well. This brings about symptoms of Minamata disease.

It was Shin-Nippon Chisso Hiryo K.K., which was located in Minamata City.

Around 1955, the Minamata factory of Shin-Nippon Chisso Hiryo K.K. was producing large quantities of a material called acetaldehyde.
Back then, there was great demand for acetaldehyde as an ingredient of plastic and other chemicals.
The acetaldehyde production processes yielded wastewater that contained harmful methylmercury, which was then discharged in great quantities into the sea, untreated.

It was found as a result of a variety of studies, including patient diagnoses, resident surveys, animal experiments and chemical analysis.

It began with the suspicion that fish contaminated with some harmful substance might be the culprit because many of the patients were fishermen, whose diet typically contains a substantial amount of fish and shellfish, and also because cats also showed abnormalities.
Then, the cause of Minamata disease was gradually brought to light on the basis of various pieces of information, including: symptoms characteristic in the patients; mercury levels in their urine; results from experiments of feeding cats methylmercury-containing food and; detection of methylmercury content in the wastewater from the factory.

Niigata Minamata disease (the second Minamata disease) occurred in the Agano River basin of Niigata Prefecture.

In 1965, nine years after the first official report on Minamata disease, a similar disease occurred in the Agano River basin.
This was caused by methylmercury contained in the wastewater from the Kanose factory of Showa Denko K.K.
These two outbreaks of Minamata disease are considered to be the four largest outbreaks of pollution-related diseases, together with Yokkaichi asthma and Itai-Itai disease.

A total of 3,000 patients have been recognized in the three prefectures of Kumamoto, Kagoshima and Niigata.

Recognition as a Minamata disease patient is given under the Act on Compensation, etc. for Pollution-Related Health Damage. As of the end of December 2024, there have been 3,000 recognized Minamata disease patients (1,791 in Kumamoto, 493 in Kagoshima and 716 in Niigata), among which 304 patients are alive (166 in Kumamoto, 48 in Kagoshima and 90 in Niigata).

In addition, there is a comprehensive medical aid program for those who are not recognized as patients but meet certain conditions, including affliction with a sensory disorder and high consumption of fish and shellfish. There are 38,320 recipients under this program (this total is in the three prefectures of Kumamoto, Kagoshima and Niigata).