They said youngsters deprived of regular sunlight are being starved of the 'sunshine vitamin', vitamin D, which is essential for healthy bones.
The record rainfall over the last three months, combined with modern lifestyles are putting children's health at serious risk.
Dr Nicola Balch, an associate specialist in child health at the British Medical Association, told the organisation's annual conference: "Modern living, with an increasingly indoor lifestyle, extended cloud cover, air pollution, modern diets and the overuse of sunscreen have reduced access to natural vitamin D."
Doctors now fear that there could be a huge rise in childhood illnesses, including rickets, fractured bones, MS and sudden infant death.
Dr Balch added: "When people aren't getting out in the sun there's going to be an increase in the amount of these vitamin D deficiency related illnesses.
"We have been aware of the problem in Scotland for a number of years. The temporary effect in the rest of the UK of heavy rainfall could have the same effect that there is north of the border.
People need just 20 to 30 minutes of sun three or four times a week to ensure they get enough vitamin D, but obviously with our weather it can be impossible to get this.
The BMA recently passed a motion calling for a national vitamin D supplement programme.
Dr Balch said: "Prevention is better than cure, and it is unlikely that the NHS will adopt a policy of prescribing holidays in the sun."
Nutritionist Leanne Olivier told the Daily Mail that nearly eight out of 10 parents are unaware of toddlers' specific nutritional needs in relation to vitamin D and the average British toddler is only getting 27 per cent of their daily vitamin D needs from their diet.
She said: "There's a reason why vitamin D is known as the sunshine vitamin - without bright light we just can't make it.
"The cloud cover on rainy days has an obvious effect on sunlight, making the sky dark and grey.
This reduction in exposure to sunlight can be really significant - especially between the ages of one and three years, when toddlers experience a huge period of growth and development and need essential nutrients to support this.