Background: Malnutrition is a serious public-health problem that has been linked to a substantial increase in the risk of mortality and morbidity. Home gardening is a part of nutrition sensitive intervention and widely used as a remedy to alleviate malnutrition. Despite the fact that children are expected to benefit from home gardening products their nutritional status is not well assessed considering this practice in Ethiopia particularly in the proposed study area. Objective: To determine nutritional status of 6-59 months of age children between households with and without home gardening practices at Zege. Methods: A community based comparative cross-sectional study was conducted among 648 paired mothers with 6-59 month children from February, 10th to march10th /2020. Simple random sampling technique was used to select study participants. Data was collected using structured pre-tested interviewer administered questionnaire. Binary logistic regression models were used to determine factors associated with nutritional status (stunting and wasting) of children. Adjusted Odds Ratio (AOR) with its 95% Confidence Interval (CI) was computed to identify statistical significant and strength of association respectively. Result: A total of 648 mothers, with their children aged 6–59 months (with response rate of 95.0%) participated in the study. Forty-eight percent (95%, CI: 44.3-52.2) and 9.6% (95%, CI:7.4-12) of children found to be stunted and wasted respectively. Being low dietary diversity (AOR= 2.7,95% CI: 1.9-3.9), Being male (AOR=2.08,95% CI:1.4-3), feeding frequency < 3/day (AOR=1.67,95% CI:1.1-2.4), and presence of diarrhea (AOR=2.6,95% CI:1.4-4.6) were risk factors of stunting. Unprotected-drinking water (AOR=2.09,95% CI:1.03-4.2), not fully immunized (AOR=2.6,95% CI:1.3-5.1) and being female (AOR=2.4,95% CI:1.3-4.6),) were predictors for child wasting. Conclusion: stunting and wasting are highly prevalent. There is no statistically significant difference in nutritional status between two households. Promoting diversified diet, access to protected water source, preventing diarrheal diseases, vaccinating children, and access to a healthy environment are vital interventions to improve nutrition. Keywords: Nutritional status under-five children, home gardening households, North west Ethiopia