The aim of this study was to investigate in 261 subjects from 58 families the association between DNA variation at the genes coding for the NaK-ATPase peptides and resting metabolic rate (RMR), respiratory quotient (RQ), and percent body fat (%FAT). Five restriction fragment length polymorphisms (RFLP) at three NaK-ATPase genes were determined: one at the al locus (BglII), two at the a2 locus (a2 exon 1 and a2 exon 21-22 with Bgl II), and two at the (3 locus (ft MspI and ft PvuII). Haplotypes were determined from the two variable sites of the a2 gene (a2 haplotypes) and the ft gene ((3 haplotypes). There was a strong trend for %FAT to be related to the RFLP generated by BglII at the a2 exons 21-22 in males (P = 0.06) and females (P = 0.05). RQ was (a) associated with the BglII RFLP at the a2 exon 1 (P = 0.02) and with the a2 8.0 kb/4.3 kb haplotype (P = 0.04) and (b) linked with the ft gene MspI marker (P = 0.04) and with the (35.3 kb/5.1 kb haplotype (P = 0.008) based on sib-pair analysis. The present study suggests that the genes encoding Na,K-ATPase may be associated or linked with RQ and perhaps with %FAT but not with RMR. (J. Clin. Invest. 1994. 93:838-843.)