Little attention has been paid to flatfish parasitism as a potential factor of variation in year-class strength. The aim of this study was to evaluate the relationship between parasitic infection and nutritional condition of young-of-year (YOY) common sole. Sole were collected monthly from May (early settlement) to November 2004 in a mussel pole culture area, using a push-net or a trawl, and dissected for parasite identification and counts. Total lipids were extracted from the whole body and lipid classes quantified. Triacylglycerols to sterols (free form) ratio (TAG/ST) was used as an index of nutritional status. Digenean metacercariae infection, characterized by two dominant genera, displayed clear seasonal dynamics and the highest records yet reported for sole. Prevalence (P%) and mean abundance (Ab±SE) increased for Timoniella spp. (Acanthostomidae) from May (P%=22%; Ab=1.9±1.1) to August (P%=100%; Ab=51.2±10.4), and for Prosorhynchus spp. (Bucephalidae) from June (P%=8%; Ab=0.1±0.0) to August (P%=100%; Ab=19.5±1.7). Epidemiological values reached a plateau after August. In this shellfish-dominated nursery area, YOY sole accumulated metacercariae in the presence of the first intermediate hosts which live in the same habitat. Total lipids decreased significantly from May to June and then remained constant until autumn, indicating a change in the proximate composition of YOY during this high growth period. Mean (±SD) TAG/ST ratio increased from very low values in May–July (0.10 on average) to a peak in September (0.57±0.31) and then fell back to values as low as before. YOY sole only stored energy as TAG prior to autumn. No relationship was found between YOY parasitic infection levels and lipid condition indices. However, the poor nutritional status and heavy infection level observed in November could dramatically lower over-winter survival of the YOY remaining in this shallow part of the nursery.