The study was to determine the role of Dietary diversity (DD), household food security (HFS), and agricultural biodiversity (AB) on stunted growth in children. Two cross-sectional studies were undertaken 6 months apart. Interviews were done with mothers/caregivers and anthropometric measurements of children 24–59 months old. HFS was assessed by household food insecurity access scale (HFIAS). A repeated 24-h recall was used to calculate a dietary diversity score (DDS). Agricultural biodiversity (AB) was calculated by counting the number of edible plants and animals. The study was undertaken in resource-poor households in two rural areas in Kenya. Mothers/Care givers and household with children of 24–59 months of age were the main subjects. The prevalence of underweight [WAZ <-2SD] ranged between 16.7% and 21.6% and stunting [HAZ <-2SD] from 26.3% to 34.7%. Mean DDS ranged from 2.9 to 3.7 and HFIAS ranged from 9.3 to 16.2. AB was between 6.6 and 7.2 items. Households with and without children with stunted growth were significantly different in DDS (P = 0.047) after the rainy season and HFIAS (P = 0.009) in the dry season, but not with AB score (P = 0.486). The mean AB for households with children with stunted growth were lower at 6.8, compared to 7.0 for those with normal growth, however, the difference was insignificant. Data indicate that households with children with stunted growth and those without are significantly different in DDS and HFIAS but not with AB. This suggests some potential in using DDS and HFIAS as proxy measures for stunting.