Drought is an important environmental factor in Mediterranean ecosystems affecting seedling recruitment, productivity or susceptibility to fires and pathogens. Studying water use efficiency in these environments is crucial due to its adaptive value allowing trees to cope with low water availability. We studied the phenotypic variability and genetic control of intrinsic water use efficiency (WUE(i)) and related traits in a full-sib family of Pinus pinaster under drought imposition. We detected significant differences in WUE(i) between clones of the same family and moderate heritability estimates that indicate some degree of genetic control over this trait. Stomatal conductance to water vapor was the trait most affected by drought imposition and it showed the strongest influence in WUE(i). Stomatal conductance to water vapor and specific leaf area (SLA) were the traits with highest heritabilities and they showed a significant genetic correlation with WUE(i), suggesting that selection of needles with low SLA values will improve WUE(i) in this species by reducing water losses through stomatal control.