Individual differences and variation in behavioural responses have been identified in many animal species. These differences may be the result of genetic or environmental factors or the interaction between them. Analysis of individual differences in behaviour may be important for many reasons. The zebrafish is a powerful model organism that is rapidly gaining popularity in behavioural brain research. However, individual differences have rarely been explored in zebrafish although significant variation in their performance has been reported. In the current study we identified individual differences in activity levels of zebrafish using a genetically heterogeneous population. Groups of zebrafish classified as high, medium, or low activity performers demonstrated consistent activity levels over a period of 7 days, and also in a subsequent open field task, suggesting stable individual differences as opposed to stochastic variation among subjects. We also uncovered a sex dependent relationship between behavioural measures. Female zebrafish in the high activity group preferred the top portion of the tank, whereas low activity females preferred the lower portion but males did not show such a relationship. The relationship between these two behaviours in females implies the potential existence of a behavioural syndrome persisting between contexts. Furthermore, females demonstrated a higher level of consistency in their behaviour as compared to males, and the behavioural differences were found to be independent of both body size and weight of the tested subjects. The identification of individual differences in activity levels in zebrafish will allow the investigation of underlying genetic and/or environmental underpinnings.