Fanconi anemia (FA) is an inherited disorder characterized by malformations, marrow failure, and predisposition to cancer. Birth defects and laboratory features are characteristic and helpful in diagnosis, when present. Chromosome fragility is pathognomonic in the diagnosis. However, in some cases, there are no obvious physical anomalies or suggestive hematologic abnormalities, and inconclusive diagnostic tests have also been described. In such cases, a molecular diagnosis is required. This approach presents some advantages, especially in populations with a high incidence of FA and of consanguinity. Herein, we present a case with mild phenotypic features, inconclusive hematological findings and a negative breakage test. The diagnosis of FA was confirmed with next-generation sequencing. To our knowledge, this is the first publication of a FA patient being molecularly diagnosed utilizing this method since its introduction. Given its technical and financial features, we suggest that next-generation sequencing might be an alternative first-line diagnostic test for selected cases from particular populations.