Environmental perfluoroalkyl substance (PFAS) concentrations have increased in the last decades, although their behaviour in the environment and potential deleterious effects are still unclear. In this context, the present study aimed to assess potential associations among these compounds in three fish species from differentially contaminated areas in southeastern Brazil, and morphometric indices used to assess environmental exposure effects, Fulton’s condition factor (FCF), the Hepatossomatic index (HSI) and the weight to length scaling coefficient (SC). Fish samples were collected from three differentially contaminated study areas in the state of Rio de Janeiro, Brazil, Guanabara Bay (GB), the Paraíba do Sul River (PS) and the Rodrigo de Freitas Lagoon (RFL). Silver scabbardfish (Lepidopus caudatus) and whitemouth croaker (Micropogonias furnieri) were sampled from both the PS (N=5 scabbardfish and N=9 croaker) and GB (N=10 for both species), while mullet (Mugil liza) were sampled from GB (N=15) and RFL (N=10). Results indicate that some of the morphometric indices seem to be directly affected by PFAS contaminant trends. Significant differences (p<0.05) among FCF were observed for mullet and croaker, while significant HSI differences (p<0.05) were observed only for croaker. The SC for each fish population varied among sampling site and fish population and did not seem to follow a fixed trend, corroborating previous assessments. A discriminant canonical analysis demonstrated higher discriminating contributions for the FCF and two PFAS, namely PFDA and PFOA. This variation is probably due to differential PFAS accumulation reflecting differences in trophic levels, although no direct associations between individual PFAS and the assessed morphometric indices were noted. PFAS, however, comprise several compounds, and each may be a different contributor to deleterious physiological effects. Further assessments are required, to better understand the potential deleterious effects of these compounds on populational fish health status.