Purpose: The aim of this study is to examine the co-occurrences of low serum ferritin and zinc and anaemia among mothers and their children in two agro-ecological zones of rural Ethiopia. Methods: Data were collected from 162 lactating mothers and their breast fed children aged 6-23 months. The data were collected via a structured interview, anthropometric measurements, and blood tests for zinc, ferritin and anaemia. Correlation, Chi square and multivariable analysis were used to determine the association between nutritional status of mothers and children, and agro-ecological zones. Results: Low serum levels of iron and zinc, anaemia and iron deficiency anaemia were found in 44.4, 72.2, 52.5 and 29.6% of children and 19.8, 67.3, 21.8, 10.5% of mothers, respectively. There was a strong correlation between the micronutrient status of the mothers and the children for ferritin, zinc and anaemia (P <0.005). Deficiency in both zinc and ferritin and one of the two was observed in 19.1%, and 53.7% of the mothers and 32.7% and 46.3%, of their children, respectively. In the 24h before the survey, 82.1% of mothers and 91.9% of their infants consumed foods that can decrease zinc bioavailability while only 2.5% of mothers and 3.7% of their infants consumed flesh foods. Conclusion: This study shows that micronutrient deficiencies were prevalent among lactating mothers and their children, with variation in prevalence across the agro-ecological zones. This finding calls for a need to design effective preventive public health nutrition programs to address both the mothers’ and their children’s needs.