The assessment of working time recording practices and their impacts on the workers’ well-being, work-life balance and health is lacking in the scientific literature with only rare exceptions. Nevertheless, this issue is becoming increasingly important especially in Switzerland. Despite the fact that the Labour Law requires to record all working hours, some categories of workers are released from this legal obligation, in particular those who benefit from more autonomy and flexible working schedules. This paper assesses the potential risk that differentiated working time regimes can have on workers’ health. The analyses are based on a sample from eight companies that apply these legal exemptions. The main outcome is that long working hours represent the main health risk factor for workers that do not record all their working hours.