For example, one Manhattan location is selling just nine breakfast food items, including McMuffins, as part of its limited menu.
On social media, some Twitter users expressed disappointment about the limited menu:
During CNBC's lunchtime visit to a Fort Lee, N.J., location on Tuesday, it took about 10 minutes to fill an order with two McMuffins, two burritos and two hashbrowns.
The store's Shift Manager Juan Garcia said all-day breakfast has caused a slowdown in operations after regular breakfast hours because the eggs take up more grill space. He estimates about 30 to 40 percent of orders have included breakfast items during the extended hours period.
Raymond Siegert, a 65-year old retiree dining there who describes himself as a loyal customer, welcomes the extended hours.
"Good—it's about time they did that," he said.
Siegert said he didn't mind the wait but thinks McDonald's should have the full menu available all day.
Only about 20 percent of markets, which are mostly in the Southeast, will serve biscuits all day while about 80 percent of markets will serve McMuffins.
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This means if you're a biscuit lover on the West Coast with a hankering for a bacon egg and cheese biscuit for dinner, you're likely out of luck.
Hashbrowns also won't be available everywhere though, spokeswoman Lisa McComb notes the "vast majority" or about 90 percent will have them.