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The objective of this study was to assess seasonal variation in nutritional status and feeding practices among lactating mothers and their children 6-23 months of age in two different agro-ecological zones of rural Ethiopia (lowland zone and midland zone). Food availability and access are strongly affected by seasonality in Ethiopia. However, there are few published data on the effects of seasonal food fluctuations on nutritional status and dietary diversity patterns of mothers and children in rural Ethiopia. A longitudinal study was conducted among 216 mothers in two agro-ecological zones of rural Ethiopia during pre and post-harvest seasons. Data were collected on many parameters including anthropometry, blood levels of haemoglobin and ferritin and zinc, urinary iodine levels, questionnaire data regarding demographic and household parameters and health issues, and infant and young child feeding practices, 24 h food recall to determine dietary diversity scores, and household use of iodized salt. Chi-square and multivariable regression models were used to identify independent predictors of nutritional status. A wide variety of results were generated including the following highlights. It was found that 95.4% of children were breastfed, of whom 59.7% were initially breastfed within one hour of birth, 22.2% received pre-lacteal feeds, and 50.9% of children received complementary feedings by 6 months of age. Iron deficiency was found in 44.4% of children and 19.8% of mothers. Low Zinc status was found in 72.2% of children and 67.3% of mothers. Of the study subjects, 52.5% of the children and 19.1% of the mothers were anaemic, and 29.6% of children and 10.5% of mothers had iron deficiency anaemia. Among the mothers with low serum iron status, 81.2% and 56.2% of their children had low serum zinc and iron, respectively. Similarly, among the low serum zinc status mothers, 75.2% and 45.3% of their children had low serum in zinc and iron, respectively. There was a strong correlation between the micronutrient status of the mothers and the children for ferritin, zinc and haemoglobin (P <0.001). There was also statistically significant difference between agro-ecological zones for micronutrient deficiencies among the mothers (p<0.001) but not for their children. The majority (97.6%) of mothers in the lowland zone were deficient in at least one micronutrient biomarker (zinc or ferritin or haemoglobin). Deficiencies in one, two, or all three biomarkers of micronutrient status were observed in 48.1%, 16.7% and 9.9% of mothers and 35.8%, 29.0%, and 23.5%, of children, respectively. Additionally, about 42.6% of mothers had low levels of urinary iodine and 35.2% of lactating mothers had goitre. Total goitre prevalence rates and urinary iodine levels of lactating mothers were not significantly different across agro-ecological zones. Adequately iodised salt was available in 36.6% of households. The prevalence of anaemia increased from post-harvest (21.8%) to pre-harvest seasons (40.9%) among lactating mothers. Increases were from 8.6% to 34.4% in midland and from 34.2% to 46.3% in lowland agro-ecological zones. Fifteen percent of mothers were anaemic during both seasons. Predictors of anaemia were high parity of mother and low dietary diversity. The proportion of stunted and underweight children increased from 39.8% and 27% in post-harvest season to 46.0% and 31.8% in pre-harvest season, respectively. However, wasting in children decreased from 11.6% to 8.5%. Major variations in stunting and underweight were noted in midland compared to lowland agroecological zones. Anthropometric measurements in mothers indicated high levels of undernutrition. The prevalence of undernutrition in mothers (BMI <18.5kg/m2) increased from 41.7 to 54.7% between post- and pre-harvest seasons. The seasonal effect was generally higher in the midland community for all forms of malnutrition. Parity, number of children under five years and regional variation were predictors of low BMI among lactating mothers. There were differences in minimum meal frequency, minimum acceptable diet and dietary diversity in children in pre-harvest and post-harvest seasons and these parameters were poor in both seasons. Dietary diversity among mothers was higher in lowland zone but was poor in both zones across the seasons. In conclusion, malnutrition and micronutrient deficiencies are very prevalent among lactating mothers and their children 6-23 months old in the study areas. There are significant seasonal variations in malnutrition and dietary diversity, in addition to significant differences between lowland and midland agro-ecological zones. These findings suggest a need to design effective preventive public health nutrition programs to address both the mothers’ and children’s needs particularly in the preharvest season.