DNA diagnostics of genetic diseases increasingly shifts towards utilization of commercial assays. Cystic fibrosis (CF)-related DNA diagnostics were used as a model for a pilot survey of the variability in the utilization of qualitative CE-marked in vitro diagnostic (IVD) assays and the scale of their modification by end users. A structured questionnaire, developed in the context of the EuroGentest project, was distributed within the frame of the 2005 annual CF external quality assessment (EQA) scheme. Its aim was to evaluate the variability in the use of different CE-marked IVD assays in routine CF DNA diagnostics. Survey results were analysed and sequentially discussed with respective users and/or manufacturers. In total, 125 responses from EQA scheme participants were received. Almost half of the respondents modified manufacturer-recommended protocols. They also reported sporadic and/or recurrent problems with assay performance and genotyping of particular alleles. Nonetheless, only half of the respondents performed in-house verification before the implementation of the assay in clinical diagnostics and/or after modification of the recommended protocol. Results of this survey substantiate the importance of guidelines for proper verification of CE-marked IVD assays in DNA diagnostics, using CF as a model.