Background: Fabry disease (FD) is a rare, X-linked inherited disorder caused by mutations in the GLA gene, which results in deficiency of α-galactosidase A (α-Gal A). This leads to the progressive accumulation of metabolites, which can cause malfunctions in systemic organs. A recent screening study in newborns demonstrated that the incidence of FD was more frequent than previously estimated and that there are still many undiagnosed or misdiagnosed Fabry patients. Therefore, the purpose of this study was to identify Fabry patients by performing high-risk screening in 18,171 individuals, enrolled from October 2006 to March 2019, with renal, cardiac, or neurological manifestations from all of the prefectures in Japan. A total of 601 hospitals from all the prefectures in Japan participated in this study. Results: From October 2006 to March 2019, 18,171 individuals with renal, cardiac, or neurological manifestations were enrolled. Low α-Gal A activity was detected in 846 individuals, with 224 of them diagnosed with FD by GLA sequencing. Cases with a family history of FD (n = 64) were also subjected to sequencing, without α-Gal A assay, as per individual request and 12 of them were diagnosed with a variant of FD. A total of 236 Fabry patients (97 males and 139 females) were detected from the 18,235 participants. There were 101 GLA variants, including 26 novel variants, detected in the 236 Fabry patients from 143 families, with 39 amenable variants (39%) and 79 of the 236 patients (33%) suitable for migalastat treatment. Conclusions: From the 18,235 participants, 101 GLA variants, including 26 novel variants, were identified in the 236 Fabry patients from 143 families. Migalastat was identified as a suitable treatment option in 33% of the Fabry patients and 39% of the GLA variants were detected as amenable. Therefore, the simple screening protocol, using dried blood spots, that was performed in this study could be useful for early diagnosis and selection of appropriate treatments for FD in high-risk and underdiagnosed patients suffering from various renal, cardiac, or neurological manifestations.