In London, two-thirds of families have been offered their first choice school
Children in about one in three families in some of England's biggest cities have not been offered a place at their first choice secondary school.
And in London the wait for information continues, as the e-admissions website for online applications is down.
Across London and Birmingham, two-thirds of pupils will start at their top preference school in September.
The proportions getting their first choices are slightly lower than last year in both cities.
But in some rural areas, more than 95% were given their first choice places.
In London thousands of anxious parents have been unable to log onto the e-admissions website for online applications which has been down since 0400 GMT.
A London Councils spokeswoman told BBC News: "We are working to fix it as soon as we can. Parents will still get a letter today."
It only affects school applications in London but 34,0000 applicants have registered online in the Greater London area.
Surrey had over 88 per cent applications online this year- so will be acutely affected by this.
More than half a million pupils across England are finding out which secondary schools they will attend next autumn.
Local councils are sending letters, e-mails and text messages to parents with details of the places they have been offered.
London: 66% offered first choice, 6% no offer from any of six choices
Birmingham: 66% first choice, 5% no offer from any of six choices
Worcestershire: 91% first choice
Leeds: 84% first choice
Sheffield: 89% first choice
Norfolk: 95% first choice
The overall national figures for England will not be available for a couple of weeks - but last year more than eight out of 10 children were allocated places in their first preference school.
London boroughs usually have the lowest rates of pupils being offered their top preference.
This year, an average of 65.7% of pupils across the capital will get their first choice school place - marginally down on last year's 66.05%.
This success rate ranged from 49% in Wandsworth to 88% in Harrow.
Across London, 88% of almost 80,000 youngsters achieved one of their top three school choices. About 6% of pupils have not been offered a place at any of their six choices - and will be allocated an alternative place.
The chairman of the London Inter Authority Admissions Group, Graham Carter, said: "For the sixth year running, London's admissions system has been able to place more than 90% of pupils at a school of their choice and two-thirds have been offered a place at their first choice school."
The relatively low rate of getting a first choice in London reflects the range of options and the popularity of some schools, which are heavily oversubscribed.
"The intense demand on certain schools inevitably means that some parents will be disappointed," says the London Councils organisation.
In Birmingham, out of almost 14,000 applicants this year, some 9,300, or 66.5%, had been offered their first-choice secondary school, down 1.4% on last year.
A further 12.3% were offered their second choice and 6.6% their third.
In Leeds, 84% of the 7,837 applying received their first preference this year, compared to 6,613 pupils, or 82%, last year. In Brighton and Hove, 2,266 pupils applied and 82% got their first choice.
In Manchester 78% of the 4,926 applying got their first preference, compared to 77% of the 4659 applying last year.
In some rural areas there is a much higher rate of pupils getting their first preference - such as Norfolk, which was above 95%.
Mary Bousted, general secretary of the ATL teachers' union, attacked the amount of attention paid to getting a first preference school place.
"As usual, the vast majority of 11-year-olds will get a place at their, or their parents', preferred school," she said.
"But we are back to Groundhog Day and the annual angst over how many pupils get into their first choice school."
Chris Keates, general secretary of the teachers' union NASUWT, also opposed the idea parents were somehow being "short-changed" if they did not get their first preference of school.
"The standards of education in all secondary schools across the country have never been higher and are continually improving.
"It is wrong to imply that because a school was not a parent's first preference, that its standards are poor."
Schools minister Diana Johnson said parents now had more choice because there were better schools and more places in them.
She said: "In 1997, a parent had a one-in-two chance of going to an under-performing school - which was totally unacceptable.
"We are now pushing all secondary schools to improve, not let them wither like in the past; we have driven up standards in failing and under-performing schools and expanded the best."
The Conservatives say their plans to allow parents to set up their own schools more easily would ease the situation. They are also calling for a simplified admissions code.