Feathers are useful for monitoring contaminants in wild birds and are increasingly used to determine persistent organic pollutants. However, few studies have been conducted on birds with known exposure levels. We aimed to determine how well nestling feather concentrations reflect in ovo exposure to hexabromocyclododecane (α-, β- and γ-HBCDD), and to determine if feather concentrations are related to physiological biomarkers. Captive kestrels (n = 11) were exposed in ovo to maternally transferred HBCDD-isomers at concentrations of 127, 12 and 2 ng/g wet weight of α-, β- and γ-HBCDD (measured in sibling eggs), respectively, and compared to controls (n = 6). Nestling growth was monitored at 5 d intervals and circulating thyroid hormone concentrations assessed at d 20. Tail feathers were collected prior to the first molt and analyzed for HBCDD isomers. The mean ΣHBCDD concentration in feathers was 2405 pg/g dry weight (in exposed birds) and α-, β- and γ-HBCDD made up 32%, 13%, and 55%, respectively of the ΣHBCDD concentrations. This isomer distribution deviated from the typical dominance of α-HBCDD reported in vertebrate samples. Exposed chicks had significantly higher feather concentrations of β- and γ-HBCDD compared with controls (p = 0.007 and p = 0.001 respectively), while α-HBCDD concentrations did not differ between the two groups. Feather concentrations of α-HBCDD were best explained by egg concentrations of β- or γ-HBCDD concentrations (wi = 0.50, 0.30 respectively), while feather concentrations of β- and γ-HBCDD were influenced by growth parameters (rectrix length: wi = 0.61; tibiotarsus length: wi = 0.28). These results suggest that feather α-HBCDD concentrations may reflect internal body burdens, whereas β- and γ-HBCDD may be subject to selective uptake. The α-HBCDD concentrations in the feathers were negatively associated with the ratio of plasma free triiodothyronine to free thyroxine (T3:T4; p = 0.020), demonstrating for the first time that feather concentrations may be used to model the effect of body burdens on physiological endpoints.