Objective: To examine changes in the prevalence of anaemia and its correlates among children of pre-school age after implementation of wheat flour fortification with multiple micronutrients in Jordan. Design: Retrospective analysis of the data from two repeated national cross-sectional panels of pre-school children. Setting: The two surveys were conducted in 2007 and 2009, 16-20 months and 34-36 months, respectively, after implementation of wheat flour fortification with multiple micronutrients in Jordan. Anaemia was considered if Hb level was < 11 g/dl. An anaemia prevalence of <= 40 % was considered a severe public health problem, while that of 20-39.9 % was considered a moderate public health problem. Subjects: A total of 3789 and 3447 children aged 6-59 months tested in 2007 and 2009, respectively. Results: The prevalence of anaemia in pre-school children declined from 40.4% in 2007 to 33.9 % in 2009 (adjusted OR= 0.74; P < 0.001). The decline in the prevalence in 2009 as compared with 2007 was more pronounced among children aged > 24 months (-13.7 points), children living in urban areas (-8.0 points), children from rich households (-9.0 points), children who had never been breastfed (-17.0 points) and well-nourished children (-6.8 points). In both surveys, presence of childhood anaemia was strongly associated with child age <= 24 months, living in poor households, breast-feeding for <= 6 months, malnourishment, poor maternal education and maternal anaemia. Conclusions: The public health problem of childhood anaemia declined from severe in 2007 to moderate in 2009, after the implementation of wheat flour fortification with multiple micronutrients in Jordan.