OBJECTIVE The 2002 Cystic Fibrosis Foundation (CFF) practice guidelines recommend adjusting for genetic potential when evaluating height status in children with CF. However, there is paucity of data to support this recommendation. We compared three methods of classifying short stature: unadjusted height percentile <10th, Himes adjusted height percentile <10th, and unadjusted height below the CFF target height lower bound. METHODS Data from 3306 children with parental heights documented in the 1986-2005 CFF Patient Registry were analyzed. RESULTS Mean height percentile of CF children (33rd) was lower than their parents' (mothers' 53rd, fathers' 57th), and 80% of CF children were below the average of their parental height percentiles. In children with short parents, Himes adjusted height percentile was significantly higher than unadjusted height percentile (27th vs. 8th), whereas the opposite was found in children with tall parents (Himes adjusted at 18th vs. unadjusted at 49th). Consequently, the prevalence of short stature decreased from 52% to 22% in children with short parents and increased from 8% to 34% in children with tall parents after Himes adjustment. In children with discrepant classification on short stature before and after Himes adjustment, percent predicted forced expiratory volume in one second was negatively associated with unadjusted height percentile but positively associated with Himes adjusted height percentile. In children with short parents, the CFF method underestimated the prevalence of short stature (9%) compared to the Himes method (22%). CONCLUSIONS Without adjustment of genetic potential, the prevalence of short stature is underestimated and the association between height and lung function is biased.