In aquatic birds, high body burdens of persistent organic pollutants (POPs) have been associated with developmental effects related to growth, increased fluctuating wing asymmetry, and disruption of the thyroid hormone, vitamin A (retinol) and vitamin E (tocopherol) homeostasis. The aim of the present study was to examine if morphological variables (body mass, liver mass, wing length, tarsus length and head length), fluctuating asymmetry of the wings and tarsus, growth rates and endocrine variables (thyroid hormones, retinol and tocopherol) were associated with hepatic levels of POPs (PCBs, OCPs and PBDEs) in 21 day old chicks of European shag (Phalacrocorax aristotelis). Partial Least Squares (PLS) analysis showed that fluctuating asymmetry of wing bone length (FA(WBL)) was affected by PCB-105, -118, -138, -153, and -180 (r(2)x=0.88, r(2)y=0.35, q(2)=0.29). Bivariate correlation confirmed significant positive relationships between FA(WBL) and each of these PCB congeners. In the PLS model no other biological variables were significantly affected by any of the POPs. Levels of POPs were much lower in the shag chicks than in eggs and in hatchlings from the same breeding colony, most likely due to growth dilution of the compounds. We suggest that the effects of the PCBs on FA(WBL) may be due to effects of these compounds on bone growth and bone structure. FA(WBL) may have functional effects on the fitness if it persists after fledging.