Salbutamol also known as the blue inhaler, could be ineffective in the case of asthmatic children carrying gene variant Arg16, say researchers from the University of Dundee and the Brighton and Sussex Medical School. The commonly used inhaler is also called Ventolin.
The study, published in the Journal of Allergy and Clinical Immunology, suggests that patients with the genetic defect, called the Arg16 variant, became less sensitive to the drug, and more prone to attacks, the more frequently it was used.
However, the team behind the study, which looked at 1,182 children and young adults in Scotland, warned that sufferers should not switch medications until more research was carried out.
"Our work does not alter current consensus guidelines for the treatment of asthma. It points towards the need for further research in this area."
However, the researchers suggested that in future children could be screened using a saliva test for the variant and offered an alternative treatment, if it can be proven to be effective in their case.
Previous studies on how the gene variant affects adults taking Ventolin have proved conflicting, Telegraph reported.
Prof Neil Barnes, from the British Lung Foundation, said that the study was "potentially significant".
However, he added that the research "requires considerable further investigation as recent large studies have shown no relationship between an individual's genetic make-up and the effectiveness of this treatment."
He added that deaths and admissions to hospital from asthma have fallen in Britain as the use of this treatment has increased, which, he said, would "strongly suggest" that the drugs were safe and effective.
Dr Elaine Vickers, research relations manager at Asthma UK, said: "The research did not look at whether a different sort of reliever asthma treatment would be more appropriate for this group of children however, so we don't yet know whether they should be given a different treatment."