The home environment is highlighted as a key determinant of children’s weight, but has not been investigated in Egypt. As a result this mixed methods study was undertaken to examine (1) relationships between the home environment and Egyptian children’s (aged 2- 12) weight (2) socio-economic differences in home environments (3) caregivers’ perceptions of obesity, and (4) children’s dietary and physical activity (PA) habits. Firstly, the Healthy Home Survey (HHS), was administered to households (n = 210) in three different SES areas in Cairo, examining the food and PA environment (including availability/accessibility and parental modelling/policies). Then semi-structured interviews with caregivers (n = 17) explored parental perceptions of obesity and children’s dietary/PA habits. The HHS indicated that after adjusting for age and gender, greater accessibility to unhealthy food (p < 0.01), less PA on weekends (p < 0.01), greater sedentary weekday activity (p < 0.01), and unhealthier parental PA modelling (p < 0.01) significantly predicted lower childhood weight. Higher SES areas and income groups had significantly better outdoor area characteristics (p < 0.001), and significantly more healthy and unhealthy (p < 0.001) food availability and greater media availability (p < 0.001). Interviews indicated that: caregivers perceived obesity as predominantly a female issue; children were defined as eating well by quantity (not quality); parents were stricter on daughters’ weights for aesthetic purposes; boys engaged in more outdoor play; PA settings differed among children from different SES areas; and unhealthy food was available in all households, but differed between SES areas in nature and affordability. This study recommends more detailed investigation of home environment variables (particularly food availability/accessibility, sedentary behaviours and cultural perceptions) on obesity in Egypt, as well as a need to initiate family based obesity awareness and intervention programmes.