This study investigated the effect of a macrobiotic (vegan-type) diet, low in calcium and vitamin D, consumed in early life, on bone mineral during adolescence. Bone mineral content (BMC) and bone area were measured in 195 adolescents (103 girls, 92 boys) aged 9–15 years, using dual-energy X-ray absorptiometry. Ninety-three adolescents (43 girls, 50 boys) had followed a macrobiotic diet in childhood, and 102 (60 girls, 42 boys) were control subjects. After adjustment for bone area, weight, height, percent body lean, age, and puberty, BMC was significantly lower in macrobiotic subjects, in boys and girls, respectively, at the whole body, −3.4% and −2.5%, spine, −8.5% and −5.0%, femoral neck, −8.0% and −8.2%, midshaft radius, −6.8% and −5.6%, and also in girls, at the trochanter, −5.8% (p < 0.05). No group differences were observed at the wrist. Group differences were not explained by current calcium intake or physical activity. We conclude that the use of a macrobiotic diet in early childhood negatively influences adjusted bone mass at age 9–15 years, observations which may hold important implications for fracture risk in later life.