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An ancestral inversion of 900 kb on chromosome 17q21, which includes the microtubule-associated protein tau (MAPT) gene, defines two haplotype clades in Caucasians (H1 and H2). The H1 haplotype has been linked inconsistently with AD. In a previous study, we showed that an SNP tagging this haplotype (rs1800547) was associated with AD risk in a large population from the Dementia Genetics Spanish Consortium (DEGESCO) including 4435 cases and 6147 controls. The association was mainly driven by individuals that were non-carriers of the APOE epsilon 4 allele. Our aim was to replicate our previous findings in an independent sample of 4124 AD cases and 3290 controls from Spain (GR@ACE project) and to analyze the effect of the H1 sub-haplotype structure on the risk of AD. The H1 haplotype was associated with AD risk (OR = 1.12; p = 0.0025). Stratification analysis showed that this association was mainly driven by the APOE epsilon 4 non-carriers (OR = 1.15; p = 0.0022). Pooled analysis of both Spanish datasets (n = 17,996) showed that the highest AD risk related to the MAPT H1/H2 haplotype was in those individuals that were the oldest [third tertile (>77 years)] and did not carry APOE epsilon 4 allele (p = 0.001). We did not find a significant association between H1 sub-haplotypes and AD. H1c was nominally associated but lost statistical significance after adjusting by population sub-structure. Our results are consistent with the hypothesis that genetic variants linked to the MAPT H1/H2 are tracking a genuine risk allele for AD. The fact that this association is stronger in APOE epsilon 4 non-carriers partially explains previous controversial results and might be related to a slower alternative causal pathway less dependent on brain amyloid load., ` The Genome Research at Fundacio ACE/Dementia Genetics Spanish Consortium (GR@ACE/DEGESCO) would like to thank patients and controls who participated in this project. GR@ACE/DEGESCO GWAS program was funded by Grifols SA, Fundacion Bancaria La Caixa, and Fundacio ACE, Institut Catala de Neurociencies Aplicades. PS-J and AR have also received support by grant PI16/01861. Accion Estrategica en Salud integrated in the Spanish National I CD Ci Plan and financed by Instituto de Salud Carlos III (ISCIII) - Subdireccion General de Evaluacion and the Fondo Europeo de Desarrollo Regional (FEDER - Una Manera de Hacer Europa). PS-J was supported by IDIVAL, Instituto de Salud Carlos III [Fondo de Investigacion Sanitario, PI08/0139, PI12/02288, PI16/01652, JPND (DEMTEST PI11/03028)], and the CIBERNED program. We thank Biobanco Valdecilla for their support. LM was supported by Consejeria de Salud de la Junta de Andalucia (Grant PI-0001/2017). DEGESCO was also sponsored by the Centro de Investigacion Biomedica en Red sobre Enfermedades Neurodegenerativas (CIBERNED, Spain). Control samples and data from patients included in this study were provided in part by the National DNA Bank Carlos III (www.bancoadn.org, University of Salamanca, Spain) and Hospital Universitario Virgen de Valme (Sevilla, Spain) and they were processed following standard operating procedures with the appropriate approval of the Ethical and Scientific Committee. The genotyping service to generate GR@ACE/DEGESCO GWAS data was carried out at CEGEN-PRB3-ISCIII; it was supported by grant PT17/0019, of the PE I+D+i 2013-2016, funded by ISCIII and ERDF. GR@ACE/DEGESCO consortia would also like to thank to all researchers contributing to this project. A complete list of collaborators involved in the GR@ACE/DEGESCO GWAS can be found at https://ciberned.es/proyectos/degesco.html.