23/03/2011 11:50 GMT | Updated 22/05/2015 10:12 BST

My Son Goes To A Church School, But I'm Not Religious

'Mrs X was talking about heaven today, are there toilets there for God and the angels?'

It was an innocent, if slightly quirky, question from my five-year-old after school one day. But as an atheist, it made me feel distinctly uneasy.

Respond that I don't believe heaven exists, and I'd be contradicting his teachers and potentially confusing him. Go along with it and I'd perpetuate a view I don't sign up to (although my son is very welcome to make his own mind up as he gets older – I don't want to indoctrinate him with my lack of belief any more than I want people who are religious to do so).

As the parent of a child at a school with a religious affiliation which does not match my own beliefs, I'm faced with this sort of thing on a fairly regular basis. I live in a borough which seems to have an ever increasing penchant for faith schools (in the last two years a new Hindu primary, a CofE secondary and a large Jewish secondary have opened their doors for the first time), and I know I'm far from alone in this situation.

Now, I can hear the cynics among you wondering whether I lied my way in by attending church for several months of Sundays and perhaps asking why I didn't just choose a non-faith school? Well, first up, I didn't feign Christianity - my son got a place fair and square under the non-churchgoer category. And secondly, of my catchment area's four primaries, three are CofE or Catholic and only one is a 'community school'. It happens to have some of the worst results in the borough. In my book, that's not much of a real 'choice'.

The fact is, sometimes the best school for your child, or the only one available if you live, say in a village with only one primary, happens to be of a faith that does not match your own. So, if you're in this situation and feel uncomfortable, what's the best way of dealing with it?

Kim Thomas, author of Primary School – A Parent's Guide says: 'Legally, you're entitled to withhold your child from religious activities, even in faith schools, but it can be very isolating for a child to be kept out of assembly when all the others attend.'

She adds that what to do depends on how strong your religious – or anti-religious – feelings are. 'However caring the school, it can be unsettling for both you and your child if they are being taught one set of beliefs in school and another at home.'

It's a very individual decision to when all this becomes such a problem that switching schools may be worthwhile, given it might mean a longer journey, worse results or unsettling your child by moving them.

For Sarah Jacobs, this point has arrived. Unable to get a place in her area's Jewish primary when her son started reception, and finding the local community school unappealing, she sent him to a C of E one. Whilst she doesn't have a great problem with him going to church and the like, her wider family struggle with the idea. 'I can swallow the fact that he comes home talking about Jesus occasionally but my parents can't and it does cause tension. As he gets older and questions things more I think it will leave him confused.' She has put him on the waiting list for the Jewish school and as soon as a place comes up will move him. 'I feel bad about taking him away from his friends but in the longer term this feels like the best thing to do.'

As for me, for now, I'm comfortable with the fact my son goes to a Christian school, even if it means there are a few awkward moments - when he declared to his teacher that 'my mummy doesn't believe in God' or when he pushes my hands together and says 'pray mummy pray!'

In my ideal world, no, he wouldn't be praying three times a day but you could argue that it makes us, as a family, think through some philosophical issues which we'd otherwise brush under the carpet. He might grow up to be a Christian, (or a member of another faith for that matter) but he might not. Do I think a few years of hymn-singing and bible reading in assemblies is going to change that? No I don't - just as they didn't for me and countless others of my generation who aren't exactly filling church pews in their droves these days.

Tips for when your family's religion doesn't match the school's:

When deciding whether to send your child to a school with a different religion to your own, be more wary if you'll be in a small minority or the only family not of that faith. Being the 'odd child out' who doesn't have a Bar Mitzvah, isn't confirmed or doesn't attend church on Sundays certainly makes things trickier.

Be careful about how you respond to beliefs and stories coming home from school which don't match your own. It's fine to clarify that this isn't everyone's view but not a great idea to declare it as out and out wrong. 'I think X, some people think Y, what do you think?' can work well.

If you have an older child who has decided they are a non-believer or wants to follow a different faith to the school's and is uncomfortable praying, suggest that they use the time for 'quiet reflection'.

·Bear in mind that all state schools – not just 'church schools' - in the UK must have a 'collective act of worship wholly or mainly of a broadly Christian nature" by law. You do have a right to remove your child from this but think carefully before doing so as it can make your child feel uncomfortable.

Some names have been changed.