We compared the analytical accuracy, times, costs and the detection rate of four procedures for the molecular analysis of cystic fibrosis (CF). DNA from 127 subjects bearing different genotypes was tested by denaturating gradient gel electrophoresis followed by sequencing (reference procedure) and, for comparison, by ASO dot-blot (in-house), reverse dot-blot (Innogenetics), ARMS (Zeneca Diagnostics) and OLA-PCR (PE Applied Biosystem). To assess inter-observer variability, all samples were tested twice. To evaluate intra- and between-series variability, two samples were tested twice in each series. All the procedures yielded reproducible results and assigned the correct genotype to each sample. ASO dot-blot is the cheapest procedure but has the longest analytical time (> 24 h) and uses radioactive labeling. It can be adapted to analyze peculiar mutations in specific ethnic groups. ARMS from Zeneca Diagnostics is rapid (4 h), easy to perform, but, except for the AF508 mutation, does not distinguish the homozygote from the heterozygote genotype. It could be used for carrier analysis in families with known mutations. OLA-PCR has the highest detection rate in most ethnic groups, is automated for capillary electrophoresis but requires a high level of operator expertise: it is suitable when collected series of samples are analyzed from large patient cohorts. Reverse dot-blot is easy to perform and can be semiautomated: it can be used as first-line screening test. Given the heterogeneity of CF mutations, commercial kits should be developed to analyze mutations peculiar to specific ethnic groups.