In association with industry, an extensive database has been established on measurements of sea louse counts on farmed Atlantic salmon for the years 1996 to 2000 from 33 Scottish fish farms. These data include extensive counts on the sea louse species, Lepeophtheirus salmonis, at various stages of the life cycle and in particular the chalimus and mobile stages. There has been considerable speculation as to what factors might affect the abundance of sea lice, much of which is based on limited evidence. Our analyses show that there is tremendous variation in sea louse infestation patterns from year to year, whereas stock type, geographical region and coastal exposure do not appear to affect mean levels of abundance. In contrast, treatments lead to pronounced cycles of sea louse infestation with peaks and troughs at 3-week intervals, and these interventions are important if the sea louse levels on fish are to be controlled. There was no evidence of water temperature affecting the mean annual abundance of sea louse infestation.