Storms and high winds of more than 65mph have battered the region damaging buildings, affecting electricity supplies, and delaying trains.
The power was cut off to 5,000 homes and businesses near Northampton, early on Thursday and to thousands of homes in Herts, Bucks and Beds.
About 1000 students at Bottisham Village College in Cambs were sent home after the gymnasium roof blew off.
East Coast Mainline services through Herts and Cambs have been reduced.
A spokeswoman for Bottisham College said the roof flew into the science block.
Port shut
"We are waiting for the gym roof to be assessed later on Thursday and will then make a decision as to whether or not the school is open tomorrow," she said.
In Northamptonshire, the M1 motorway was blocked northbound at junction 19 after a lorry tipped over onto its side, blocking all three lanes.
EDF Energy said nearly 25,000 customers were affected in Hertfordshire, about 1,800 in Buckinghamshire and 240 in Bedfordshire.
EON also said thousands of its customers were affected, although it could not say whether any of them were in the parts of Beds and Bucks it serves.
The Queen Elizabeth II bridge at the Dartford Crossing, which links the M25 between Essex and Kent, has been closed because of high winds.
Southbound traffic diverted through one of the tunnels which normally carry only northbound vehicles.
Felixstowe's container port in Suffolk has also been shut because of 50mph winds but the roll on roll off services have been operating as normal.
Trees have been uprooted in parts of Norfolk by the winds.
The Highways Agency is asking drivers to think twice about journeys if the weather is too severe.
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