Menstrual cycles are an important biological marker in reproductive toxicology but the effects are frequently not distinguishable from the effects of inadequate nutrition which are synergistic. The delay in ovulation and slow-down of the menstrual cycle are the main effects associated with an increased risk of subsequent miscarriage, low birth-weight and congenital malformations. Irregularity of cycle length is also a biological effect marker. There is an enhanced risk during recovery from amenorrhoea of continued long cycles and recovery should be monitored by recording cycle length at least. Amenorrhoea or slow-down of the menstrual cycles are non-invasive markers of depressed levels of steroid hormones which can result in poor pregnancy outcome and which can be damaging to bone maintenance in the longer term.