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Individuals with random left–right departures from bilateral symmetry are predicted to exhibit fitness reduction including increased parasitism. In an insular lake population of stickleback (Gasterosteus aculeatus) from the Queen Charlotte Islands, Western Canada, phenotypes with high or low number of lateral bony plates exhibited increased plate asymmetry relative to modal phenotypes. Asymmetric lateral plate phenotypes had increased prevalence and to a lesser extent intensity of parasitism relative to symmetric individuals, suggesting that differences in genetic resistance to pathogens contributed to unequal parasitism. The effect occurred mainly in the larger adults and during the warmest season, which may be due to the high metabolic costs incurred during the summer breeding season. Dietary differences between symmetric and asymmetric phenotypes were also detected and could contribute to unequal infection rates by mediating exposure to infected prey items. Our study, which is one of the first long-term field assessments of asymmetry and parasitism, yields results that are consistent with studies linking asymmetry to reduced fitness and indicate that lateral plate asymmetry can be an indicator of poor individual quality, despite its apparent directionality.