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Despite hypothesized concerns about deterioration beginning in adolescence, longitudinal data and associated factors regarding standardized assessment of physical functioning are not available for Fontan patients. Parents who participated in the Fontan Cross-Sectional Study completed the Child Health Questionnaire at 2 time points for 245 subjects ages 6–18 years. Associations between change in Physical Functioning Summary Score and baseline patient, medical, and laboratory characteristics (mean age 9.5 ± 1.7 years) and follow-up patient and medical characteristics (mean age 16.2 ± 1.6 years) were determined by regression analyses. During a mean of 6.7 ± 0.4 years, a small (not clinically important) but statistically significant decrease in score from 46.2 ± 11.7 to 44.5 ± 12.1 (p < 0.03) was noted. Subjects with higher baseline scores had a greater decrease in score (r = −0.48; p < 0.001). A multivariable model of patient and medical characteristics (R2 = 0.11) showed that a greater decrease in score was significantly associated with interim development of asthma (n = 13; parameter estimate [PE] −6.6; p < 0.05) or other chronic respiratory, lung, or breathing problems (n = 13; PE −12.5; p < 0.001) and the presence of protein-losing enteropathy at any time (n = 12; PE −9.4; p = 0.006). Change in score was not significantly associated with baseline laboratory measures of exercise capacity and ventricular characteristics and function. Therefore, although physical functioning may be stable during adolescence for many Fontan patients, deterioration occurs in some in association with respiratory conditions and protein-losing enteropathy. Further longitudinal study is necessary to better understand the relationship between clinical morbidities and functional health status as these patients transition into adulthood.