A parasitological investigation was performed on a total of 5380 Atlantic cod larvae, post-larvae and small juveniles sampled from the North Sea during a period of five years. The copepod Caligus elongatus (Von Nordmann, 1832) and the nematode Hysterothylacium aduncum (Rudolphi, 1802) were found at a relatively high prevalence of infection (4.6% and 5.2%, respectively). The infection by both parasites showed annual and spatial variability. C. elongatus showed a higher prevalence in 1992 compared to the following years, whereas the prevalence of H. aduncum increased from 1992 to 2001.We observed a relation between parasite distribution and parameters such as latitude and water depth. Adult digeneans (Lecithaster gibbosus and Derogenes varicus) and larval cestodes were also found with lower infection rates. Since changes of infection levels coincided with increasing North Sea water temperature in the studied period, it is hypothesized that temperature may affect parasite population levels. However, it is likely that other environmental factors may contribute to the observed variations. Absence of infection intensities higher than one nematode per fish in small larvae and post-larvae suggests that host survival may be affected by a high infection pressure. The relatively high levels of infection in the younger stages of cod, and the annual/spatial variability of these infections should be considered in the understanding of the early life dynamics of the species.