Madeleine's parents, Kate and Gerry McCann, walked hand-in-hand to a service near their home in Rothley, central England. They made no comment to the media.
In Portugal's Algarve region, worshippers, including Gerry McCann's brother John and other family members, packed a 19th-century beach-side chapel in Praia da Luz for an evening Mass in English and Portuguese. A message written by Kate McCann was read out in both languages.
Madeleine disappeared during a family vacation in Praia da Luz on May 3 last year, a few days before her fourth birthday.
Police have named the McCanns and a local man, Robert Murat, as formal suspects in the case. All deny involvement in her disappearance, and police have not decided whether to file charges - or drop the case.
"At this stage, nothing has been determined regarding possible charges or closing the case," Alipio Ribeiro, head of the Policia Judiciaria investigative department, told the Portuguese national news agency Lusa. Police are still gathering and analyzing evidence, he said.
Portugal's Attorney-General Fernando Pinto Monteiro said about 1 million children go missing each year worldwide, and only around 20 percent of them are found.
"We may yet find out what happened. Let's wait until the investigation is complete," Pinto Monteiro was quoted as saying by Lusa.
"But if we fail, it won't bring any disgrace for the Portuguese police. Unfortunately, it happens everywhere," he said during an official visit to northern Portugal, according to Lusa.
The McCanns, who have launched an online campaign to find their daughter, returned to England in September, a few days after they were named as suspects.
Madeleine's uncle John said Kate and Gerry had decided to spend the anniversary at home with close friends and the girl's younger twin sister and brother.
"Associated with Praia da Luz is a lot of pain, a lot of emotional turmoil and it's a hard time for them," John McCann told reporters on the beach front. "Anybody who likes children, who has their own family ... you can feel that pain as well."
He said the anniversary had brought a "huge upsurge" in traffic to the Find Madeleine Web site. He handed out leaflets in Portuguese that appealed to people to provide any information they might have, either by phone or e-mail, and promising anonymity and confidentiality to those who sought it.
In England, the Archbishop of York penned a special prayer for Madeleine to mark the anniversary.