The aim of this study is to investigate the effectiveness of a worksite health promotion programme by individual counselling on sick leave. Three municipal services of Enschede, the Netherlands, participated in this trial. A total of 299 civil servants were measured at baseline and were randomised by cluster into the intervention (n = 131) or the control group (n = 168). During nine months, subjects in the intervention group received a total of seven consultations, particularly aimed at increasing their physical activity level and improving their dietary habits. Both the intervention and the control subjects received written information as to several lifestyle factors. Sick leave data regarding the nine month intervention period (from May until January) were collected from each municipal service's personnel department. In addition, sick leave data concerning the nine month period pre- and post-intervention were collected. Results showed no significant effect of individual counselling on sick leave. Continued research investigating the effectiveness of this individual counselling programme on several health related outcomes is useful to clarify the trend observed in sick leave.