OBJECTIVES: To compare the expected costs (EC) of three different screening strategies for cystic fibrosis implemented in Spain: TIR/DNA/DGGE, TIR/TIR/DNA, and TIR/DNA. These strategies correspond to screening programs in Basque Country, Castilla León and Canary Islands.  METHODS: For each strategy, EC per child screened, also EC per infant with CF and EC disaggregated by type of test was estimated. In addition, sensitivity of each strategy was calculated. Unless there are differences between unit cost along communities, the same unit cost source for all programs was used, in order to allow comparisons. RESULTS: The estimated EC per screened neonate were € 3.67, € 4.07, € 4.11 for TIR/ADN, TIR/ADN/DGGE, and TIR/TIR/ADN respectively, showing that TIR/ADN/DGGE is the strategy with lowest EC for its population. Regarding the sensitivity of the three strategies, the results showed similar and high values for all of them, being the strategy of Basque Country which had highest value (99.37%). The ECs per neonate suffering CF were 82.703,48 €, 18.726,29 €, 16.604,10 € for TIR/ADN, TIR/ADN/DGGE, and TIR/TIR/ADN respectively, showing highest cost per neonate with the disease, however the power of this results is still low, and there are differences between incidences along strategies. CONCLUSIONS: In this cost comparative study it was obtained that the most expensive screening program in term of population ECs is TIR/TIR/ADN. However, this strategy has the lowest EC/neonate with CF. In the opposite TIR/ADN has the lowest EC in term of population but the highest cost in term of neonates with CF. However more data are needed in order to increase the power of estimations.  It is clear that the factors which have most influences in cost difference between regions are algorithm type used, order of diagnostic tests and cutoff points.