The aim of the study is to evaluate the prevalence of iron deficiency anaemia (IDA) after a wheat flour fortification program with electrolytic elemental iron in Morocco. Two surveys were conducted after introduction of fortified wheat flour. The target population was women aged 15–49 years and preschool children aged between 2 and 5 years. A total of 1,258 and 1,237 children aged between 2 and 5 years, and 1,497 and 1,537 women of childbearing age have been involved, respectively, in the first and second investigation using a sentinel system. Ferritin and C-reactive-protein analyses were determined in a sub-sample of 268 and 130 women who were selected in May 2006 and January 2008, respectively and, in a subsample of 146 and 201 preschool children who were recruited in May 2006 and January 2008, respectively. The prevalence of anaemia in women was 31.5 and 33.3 % in May 2006 and January 2008, respectively. The prevalence of IDA was 63.9 and 59.1 % in May 2006 and January 2008, respectively. The prevalence of anaemia among preschool children was 47.8 and 37.5 % in May 2006 and January 2008, respectively. The prevalence of IDA in preschool children was 16.7 and 16 % in May 2006 and January 2008, respectively. The flour fortification programme with electrolytic elemental iron in Morocco had no apparent beneficial effect on the prevalence of IDA among women of childbearing age and preschool children.