The gales cut rail links between Bury St Edmunds and Cambridge when a tree fell on the line at Kennet.
Suffolk Police say they are getting reports of trees coming down on rural roads across the county.
Greater Anglia Trains epected to have coaches running between Bury and Cambridge by 4.15pm, but Network Rail staff had managed to clear the obstruction by then.
However, Greater Anglia says trains are being delayed by about 30 minutes while it ‘recovers the service’.
There are also 30 min delays on services running through Shippea Hill station, which affects those to Lakenheath and Brandon.
The police said the A143 at Great Barton near the Bunbury Arms was partially blocked by a fallen tree for a time but is clear again.
Check train service disruption at www.journeycheck.com/greateranglia
The Highways Agency also reports an incident on the A14 at junction 55, the A12, which is part of the diversion route for the Orwell Bridge, which closed at 2pm due to high winds.
For more on the weather see our main weather story