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Polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are ubiquitous environmental chemicals that have long half-lives. Humans are exposed to PCBs and PBDEs mainly through diet, and relative to other populations, those who consume sport-caught fish generally have elevated body burdens. Numerous studies have found associations between prenatal exposure to these chemicals and neurodevelopmental deficits, but there are few studies assessing the impact of exposure during adolescence, a period of rapid development of executive functions. We assessed executive functions in adolescents at risk for exposure to PCBs and PBDEs through consumption of fish from the Lower Fox River and other contaminated waters in northeastern Wisconsin. Between 2007 and 2012, a sample of 115 12–18-year-old children was recruited from households in the Green Bay, WI area in which at least one parent held a WI fishing license. We assessed associations of total PCBs and total PBDEs, as well as the predominant individual congeners (PBDE 47 and 153; PCB 138/163, 153 and 180) with performance on four tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB): Intradimensional/Extradimensional Set-Shifting (ID/ED) which assesses cognitive flexibility, Delayed Matching to Sample (DMS) which assesses visual recognition memory, Spatial Working Memory (SWM), and Stockings of Cambridge (SOC) which assess planning and working memory. In addition to the exposure and outcome variables, multivariable regression models included the child’s age, sex and IQ score as well as a sex by exposure interaction term. All of the children were non-Hispanic whites and most parents were married, employed, and had at least some college. After adjusting for serum lipids, the GM (GSD) for total PCBs (ng/g) was 30.83 (2.46), and the GM (GSD) for the predominant PCB congeners PCB 138/163, PCB 153, and PCB 180 were 4.60 (2.39), 5.43 (2.37), and 1.01 (2.71), respectively. The GM (GSD) for total PBDEs (ng/g) was 26.82 (3.30), and the GM (GSD) for the predominant PBDE congeners PBDE 47 and PBDE 153 were 16.64 (2.94) and 3.95 (3.43), respectively. For both chemicals, the primary finding of the negative binomial regression analyses was that higher blood serum concentrations were associated with poorer cognitive flexibility as measured on the ID/ED task. In particular, the PCB x sex interaction p-value was 0.08, and stratifying by sex demonstrated that males with higher blood serum total PCB concentrations (β = 2.20, 95% CL: 1.16, 4.16, p = 0.02) took more trials to complete the ID/ED task, while both males and females with higher total PBDE concentrations (β = 1.74, 95% CL: 1.25, 2.42, p = 0.001) took more total trials to complete the task. Higher serum total PCB concentrations were also associated with more errors on the DMS task (β = 1.15, 95% CL: 1.00, 1.31, p < 0.05). These findings suggest that exposure to PCBs or PBDEs during adolescence may be associated with impaired cognitive flexibility and that adolescent PCB exposure may be associated with visual recognition memory deficits.