Objectives: To compare performance of weight-for-length and body mass index as estimators of undernutrition in children with cystic fibrosis (CF). Study design: We analyzed pediatric anthropometric data from the Cystic Fibrosis Foundation Patient Registry. Undernutrition was defined by weight-for-length z score (WFLZ) or body mass index z score (BMIZ) ≤–1 (15th-percentile). Group 1, reference group, consisted of subjects with both BMIZ and WFLZ >–1; group 2: BMIZ ≤–1 and WFLZ >–1; group 3: BMIZ >–1 and WFLZ ≤–1; and group 4: BMIZ and WFLZ ≤–1. Group differences in length-for-age-Z across ages 2-24 months were tested using generalized estimating equations. The association of group at age 2 months with BMIZ <–1 at age 6 years was tested using logistic regression adjusted for demographic and disease characteristics. Results: Overall, 163 482 anthropometric measurements were available from 12 640 individuals, of whom 16.8% were discordant for undernutrition status at age 2 months. Discordance (1.5%-10%) was less common with increasing age. Length-for-age-Z was lower in group 2 than group 1 and group 3 between birth and 24 months (P <.05). Odds of WFLZ-defined undernourished at 2 months were lower for shorter individuals (OR 1.5, CI 1.4-1.6, P <.001). Undernutrition risk at age 6 years was greater for group 2 vs group 3 (OR 1.9 vs 1.0, P <.001). Conclusions: Infants with cystic fibrosis classified as undernourished by BMIZ, but not WFLZ, had greater risk of undernourished status later in childhood. Infants with low BMIZ but normal WFLZ tended to be shorter, suggesting BMIZ may better capture undernourished status than WFLZ in shorter infants.