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Background: Recessive Stargardt disease is due to mutations in the retina-specific ABC transporter gene. Established strategies for molecular characterization of this gene include direct detection by a microarray interrogating approximately 500 DNA variations and a scanning denaturing HPLC methodology. Methods: Because 11 mutations were reported to account for approximately 50% of molecular defects in the Italian population, we evaluated an alternative open microchip-based assay for a fast and simplified level 1 screening for these mutations. Results: This approach allowed the characterization of both mutated alleles in 4% and one mutated allele in 43% of cases when applied to a cohort of 47 Stargardt patients. In the same patients, further investigation by denaturing HPLC for complete characterization identified both mutated alleles in 51% and one mutated allele in 19% of cases, allowing the detection of 38 different mutations, five of which had never been described. Notably, new mutations account for a high proportion (13%) of molecular defects in our patient cohort. Conclusions: This finding raises the question about the choice of the optimal diagnostic strategy for complete genotyping of the ABCA4 gene, as new mutations could not be identified by any direct detection technology, irrespective of the total number of variations screened.