Members of the Rail, Maritime and Transport union (RMT) at Southern, Merseyrail and Arriva Rail North walked out amid worsening industrial relations in the industry.
Picket lines were mounted outside stations across the country.
The Southern dispute started more than 16 months ago, with the RMT now taking 34 days of strike action.
Southern said it planned to run most services despite the strike, although there will be a number of cancellations.
The number of Merseyrail and Arriva Rail North trains will be reduced. Services at both companies will mainly run between 7am and 7pm.
RMT general secretary Mick Cash said. "These strikes are about putting passenger safety before private profit, and those that seek to undermine the safety culture on our railways in order to fill their own pockets should be called to account and forced back to the negotiating table.
"The resilience and determination of our members in the three separate disputes over passenger safety is right at the forefront again this morning.
"Support remains absolutely solid in all areas as RMT members continue the fight to put safety and access before private profit on Britain's railways. It's now time for Chris Grayling (Transport Secretary) and this minority Government to stop the great British rail rip-off, end the wholesale destruction of our rail safety culture and force his private contractors back to the negotiating table."
Paul Plummer, chief executive of the Rail Delivery Group, which represents train companies and Network Rail, said: "Train companies are doing all they can to keep passengers moving on the day many students return to school or college, and people are going back to work.
"Rail companies are working hard to upgrade the railway to support passengers and our economy now and for the long term, including 6,400 more services a week by 2021."
The threat of industrial action against the industry's newest franchise holder is also looming.
RMT members on South Western Railway are to be balloted for strikes, just days after the operator took over the running of services from London Waterloo.
Southern services were further disrupted by a signal failure at Redhill in Surrey.