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Starting today, a new Clipper card will cost adult transit riders $3.

The blue and white cards used by riders of BART, Muni and other Bay Area transit lines have been free since their introduction in June 2010, to encourage residents to adopt the new system. However, a minimum balance of $5 was required in order to use the cards. With the new fee, the minimum balance will no longer apply to new adult cards.

The new fee doesn’t apply to youth and senior Clipper cards, which remain free.

The fee will also be waived for new customers who sign up for automatic reloading when ordering a Clipper card online.

The $3 charge “helps offset the actual cost of producing the card” and “encourages people to keep and reuse their cards, not dispose of them,” according to a statement posted on the San Francisco Municipal Transportation Agency’s website.

Some commuters aren’t thrilled by the change.

The new fee is “arbitrary” and “weird,” said Kyle Garrett, 30, who was propped against a lamppost while waiting at the corner of 16th and Mission for an Oakland-bound bus.

“It really speaks to the trend of rising costs in the city. The cost to ride transportation is disproportionate to the cost of living,” said Garrett.

“I guess it’s too bad for people who need a new Clipper card,” said Brian Amanaos. “When I first got the card I was surprised that it was free. I guess that means I can’t lose my card,” added the 26-year-old engineer.

“We want to encourage people to keep their cards, reload them automatically and use them for a long time, rather than throwing them out and getting new ones,” said Carol Kuester, director of the Metropolitan Transportation Commission’s electronic payment division. “Charging a fee for the card also helps us be better stewards of public funds.”

Brian Riccardi was more concerned with the time it takes for new funds to be applied to his Clipper card via the autoload function. “They tell you it will take three to five days but it takes a lot longer than that,” said Riccardi, who was waiting for a bus to downtown San Francisco.

In July 2012, more than 15 million trips were taken using Clipper cards. More than 600,000 people use the card on an average weekday.

The new fee comes on top of fare hikes for Muni and BART as of July 1.

For more information on the fare changes, click here.