Government data, which goes back to 1964, shows that almost all the disappearances have occurred since 2007, when then-President Felipe Calderón launched his "war on drugs".
The United Nations has called it "a human tragedy of enormous proportions".
Many of the missing are victims of organised crime and hardly any of those responsible are punished.
The latest update to the national registry of missing people kept by Mexico's attorney general's office shows that over the past two years, the number of disappeared has risen from 73,000 to more than 100,000.
Three quarters of those reported missing were men and one fifth were under the age of 18 at the time of their disappearance.
Relatives of the disappeared say that the government is not doing enough to find them, and that officials are indifferent when they report their loved ones missing.
Many have taken matters into their own hands, digging up unmarked graves in the hopes of finding remains of their loved ones.
On 10 May, the day Mexicans marked Mother's Day, hundreds of women took to the streets to demand the authorities do more to locate the missing and punish those behind enforced disappearances.
According to the UN, only 35 of the recorded disappearances have led to the conviction of the perpetrators.
It said that the "staggering rate of impunity" was mostly to blame on the lack of effective investigations.
"It leaves victims' families, already deeply affected by the disappearance of their loved ones, to cope alone with the additional burden of trying to ascertain what happened to them," the Office of the High Commissioner for Human Rights said in a statement.
In a report published last month, the UN Committee on Enforced Disappearances said that organised crime had become a "central perpetrator" of disappearances in Mexico "with varying degrees of participation, acquiescence or omission by public servants".
Rights group Centro Prodh asked on Twitter "how many more have to go missing for the government to come up with a policy to prevent and eradicate disappearances".
The state with the highest number of disappearances is Jalisco, where the Jalisco New Generation Cartel has its power base.
In recent years, migrants have increasingly been among those reported missing.
Last year, 349 foreign nationals were reported as disappeared, compared to 89 the previous year, according to a report by the Jesuits' Missing Migrant Search Program (SJM).