An experiment was performed to determine whether boron deprivation would adversely affect vertebra (trabecular) bone microarchitecture, and whether any adverse effect would be modified by dietary fatty acid composition. Female rats were fed diets containing 0.1mg (9 micromol) boron/kg in a factorial arrangement with variables of supplemental boron at 0 (boron-deprived) or 3 (boron-adequate) mg (278 micromol)/kg and fat sources of 75 g safflower oil/kg or 65 g fish (menhaden)oil/kg plus 10 g linoleic acid/kg. After 6 weeks, six females per treatment were bred. Dams and pups continued on their respective diets through gestation, lactation, and after weaning. At age 21 weeks, the microarchitecture of the fourth lumbar vertebrae from 12 randomly selected pups from each treatment was determined by microcomputed tomography. Boron deprivation decreased bone volume fraction and increased trabecular separation and structural model index. Boron deprivation decreased trabecular thickness when the dietary oil was safflower. A three-point bending test for bone strength found that boron deprivation decreased the maximum force needed to break the femur. Feeding fish oil instead of safflower oil decreased connectivity density in vertebrae of boron-deficient but not in boron-adequate rats. Fish oil instead of safflower oil increased the maximum force to break and the bending moment of the femur, especially in rats fed adequate boron. The findings confirm that boron and fish oil are beneficial to cortical bone strength, and show that nutritional intakes of boron are beneficial for trabecular bone microarchitecture and influence the beneficial effects of fish oil on bone.