The exceptional growth rate during adolescence demands increased dietary intake. We aimed to compare diet and lifestyle of pre-adolescents with height and weight below the 10th percentile, with those of pre-adolescents of higher height and weight. This case-control study included healthy pre-pubertal girls (≥9 years) and boys (≥10 years). The case groups included 31 girls and 32 boys with height and weight <10th percentile, and weight percentile ≤height percentile. The control groups comprised 24 girls and 24 boys, with height ≥25th percentile, BMI 5th-85th percentiles. Participants completed 3-day food diaries and lifestyle-related questionnaires. Energy intake/estimated-requirement and protein/body-weight were comparable in the case and control groups, both in boys and girls. In boys, fat (P = 0.050) and carbohydrate (P ≤ 0.001) intakes/body-weight were higher in the case group versus controls; and iron (P < 0.001), zinc (P = 0.005), vitamin A (P < 0.001), calcium (P = 0.005), and vitamin C (P = 0.034) consumption were lower. In girls, carbohydrate/body-weight was higher in the case group compared to controls (P = 0.007); micronutrient intake was comparable, and lower than recommended. Compared to controls, short and thin boys reported less sleep during weekdays (P < 0.001). Relatively short, thin pre-adolescents may have distinct dietary intake and sleeping patterns compared to taller peers, especially boys. Nutrition is a key environmental determinant of childhood growth. Not much is known about late nutritional impact on growth in children whose anthropometric indices are below the 10th percentile. We compared food diaries and lifestyle questionnaires of pre-pubertal pre-adolescents with height <10th percentiles and weight≤height for age and sex, with those of peers with indices in higher percentiles. We found distinct differences in micronutrient intakes and sleep duration in the shorter boys, but no energy deficit in either sex. We suggest that diet and lifestyle parameters should be evaluated in children with relatively low anthropometric indices, to ensure optimal growth.