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Objectives In North Africa, due to the rapid nutrition transition, the within-subject double burden of excess adiposity and anemia or iron deficiency (ID) is prevalent, especially among women. Contrasted hypotheses on iron content of the nutrition transition high energy diets could result in either aggravating or protective co-ocurrence. We studied its nature, strength and variation with sociodemographic characteristics among women of childbearing age. Methods Two cross-sectional studies used stratified clustered random samples of 20–49 y. urban women in 2009/2010 in Rabat-Salé, Morocco (n = 811) and Tunis, Tunisia (n = 1689). Excess adiposity (EA) was assessed by Body Mass Index ≥30 kg/m2, or Waist Circumference ≥88 cm or Fat Mass (derived by impedancemetry) ≥39, 40 or 41% (depending on age and country). ID was ferritin <15 µg/L (corrected for inflammation), anemia was Hb < 12 g/dL. A purposely developed symmetrical measure of co-occurrence was used: IPR (Independence Probability Ratio) e.g., for ID IPR = P(EA&ID)/[P(EA)xP(ID)] = 1, <1 or >1 respectively in case of independent, protective or aggravating within-subject co-occurrence. IPR crude or adjusted were estimated using multinomial logistic models. Results are presented with P = 0.95 confidence intervals. Results The nature of EA co-occurrence with anemia or ID varied according to EA indicator and country but with most of them being independent. Nevertheless, protective co-occurrences were found between Fat Mass and anemia (IPR = 0.84[0.68–1.00] in Morocco and also in Tunisia 0.75[0.63–0.89]), and especially for non-ID anemia (IPR = 0.67[0.53–0.82] in Tunisia). On the other hand, none was found with ID (IPR = 0.97[0.89–1.05] in Morocco, IPR = 1.04[0.86–1.23] in Tunisia). Variation with socio-demographic characteristics was mild. Conclusions The results somewhat refute hypotheses on the within-subject non-independent co-occurrence of EA rather with ID or ID anemia, in relation with iron content of nutrition transition diets in the context. Beyond genetic causes of non-ID anemia, hypotheses linked to other nutrients and/or physiological pathways must be considered. Funding Sources French Ministry of Foreign Affairs (CORUS Program), INNTA (Tunisian National Institute of Nutrition), IRD (French National Research Institute for Sustainable Development).