The objective of the present study was to assess the association between individual genetic variants and haplotypes of several obesity-related genes (FTO, MC4R, MTCH2, NEGR1, SEC16B, INSIG2, TMEM18, KCTD15, SH2B1, FAIM2, ATXN2L, BDNF, BDNFOS, GNPDA2, ADRB2, PRL, PTER, ADIPOQ, ETV5, MAF, NPC1, CTNNBL1, and HTR2C) and BMI in two Spanish populations. The gene discussed is FTO; the disease is obesity due to melanocortin 4 receptor deficiency.