The doubly labeled water method for measuring total energy expenditure is subject to error from natural variations in the background ²H and ¹⁸O in body water. There is disagreement as to whether the variations in background abundances of the two stable isotopes covary and what relative doses of ²H and ¹⁸O minimize the impact of variation on the precision of the method. We have performed two studies to investigate the amount and covariance of the background variations. These were a study of urine collected weekly from eight subjects who remained in the Madison, WI locale for 6 wk and frequent urine samples from 14 subjects during round-trip travel to a locale 500 miles from Madison, WI. Background variation in excess of analytical error was detected in six of the eight nontravelers, and covariance was demonstrated in four subjects. Background variation was detected in all 14 travelers, and covariance was demonstrated in 11 subjects. The median slopes of the regression lines of ²H vs. ¹⁸O were 6 and 7, respectively. Modeling indicated that ²H and ¹⁸O doses yielding a 6:1 ratio of final enrichments should minimize this error introduced to the doubly labeled water method.