The Parliamentary Group for Muscular Dystrophy says it is concerned about funding for high-cost drugs.
It comes after the special budget for treating rare diseases in England was merged into the overall NHS budget. Scotland has a fund in place for the so called "orphan drugs" until April 2014.
A UK-wide strategy for rare diseases will be published this year.
Overall it is estimated that 3.5 million people in the UK suffer from a rare disease, and that 70,000 of those have some form of the different muscle-wasting diseases known as muscular dystrophy.
The MPs say they are concerned that funds previously ear-marked for drugs for rare diseases have now been merged into the budget for all specialised services in England.
Decisions on how to spend a Â£100m fund for rare diseases, sometimes called orphan conditions, were made on the advice of a special committee but that power was transferred to NHS England in April.
At the same time, the cost and clinical advisory body, the National Institute for Health and Care Excellence (NICE), took over responsibility for assessing these drugs as part of the wider reorganisation of the health service in England.
Concerned MPs warn the way drugs are funded and assessed could lead to hundreds of children with life-shortening conditions being denied rapid access to new therapies.
They want a drugs fund for rare diseases, similar to the one in Scotland, and a rapid system for regulators to review cutting edge drugs.
The chairman of the all-party group, Dave Anderson MP, said: "We have seen that successfully developing an effective treatment is far from the end, with agonising waits for some families through licensing and funding issues."
Most of those affected by rare diseases are children, and the charity, Rare Disease UK, estimates that 30% die by their fifth birthday.
For the first time there are some promising developments on the horizon for one condition, Duchenne Muscular Dystrophy. The results from some final-stage clinical trials of a genetic therapy are expected later this year, and may offer the hope of new treatments.
Robert Meadowcroft, chief executive of the Muscular Dystrophy Campaign, said they were gravely concerned at the lack of a dedicated fund or clear criteria for how new drugs might be assessed.
"We've got families setting great store by the treatments coming through. It would be heartbreaking and devastating if they're not available to children who need them."
NICE said it accepted it needed to develop a different approach for looking at rare conditions, adding: "Our process and methods for developing guidance for such drugs will ensure that patient and clinical experts are involved."
Negotiations are under way with the pharmaceutical industry on a new pricing regime which would include a new way of recognising the value of some new treatments.
A Department of Health spokesman said: "We are working closely with other health departments and stakeholders to develop a UK strategy for rare diseases. This will be published by the end of the year."

16 January 2016 Last updated at 12:15 GMT
The CCTV, recorded on 5 January, shows the HGV passing the van at speed near Ulceby, forcing the van driver to stop on the crossing.
Inspector Graham Bridges said it was an example of "extremely dangerous driving" and the police are now trying to trace both drivers.

Officers said the 24-year-old had been detained in police custody in connection with a serious sexual assault in Queen's Park on 30 March.
The park, at Pollockshaws Road and Balvicar Street, was cordoned off while police investigated the incident.
A report will be submitted to the procurator fiscal, Police Scotland said.
A group of MPs is calling for a ring-fenced fund to pay for drugs for rare conditions.
[NEXT_CONCEPT]
Footage of a lorry overtaking a van on a level crossing in Lincolnshire has been released by British Transport Police.
[NEXT_CONCEPT]
Police investigating the rape of a 37-year-old woman in a popular Glasgow park have arrested a man.