Background: Social, emotional and behavioural development in early to middle childhood impact upon many outcomes in future life and are influenced by home, neighbourhood and school environments. We used linked data to investigate differences between areas in Glasgow City in level of difficulties in pre-school age children, after consideration of demographics, including area-level deprivation. Methods: Pre-school education staff completed Strengths and Difficulties Questionnaires (SDQ) on all children progressing to school from a local authority or partnership (local authority-funded private) pre-school in Glasgow City between 2010 and 2012. These data were linked to individual (age, gender) and area-level (deprivation) demographics from the City Council Education Services Department. Statistical models were fitted to the SDQ scores, adjusting for age, gender, area deprivation, year of school entry, pre-school establishment attended and electoral ward of residence. Correlation between neighbouring wards was incorporated to allow for clustering of scores. Results: Boys and those living in more deprived areas had higher levels of difficulties. Children aged 5.0-5.5 years had fewest difficulties, while the oldest and youngest children had similar levels of difficulties. There were no significant secular trends by year of school entry. There remained differences among areas after adjusting for these variables, with children living in some areas having fewer difficulties than would be expected based on their socio-demographic characteristics. Conclusions: There remained differences in children’s levels of difficulties between areas after adjusting for age, gender, area deprivation and year of school entry. Children in some very deprived areas had fewer difficulties than might be expected, while those in relatively affluent areas had more difficulties than expected based on their deprivation level. There may be other, unmeasured, individual- and area-level reasons for children’s level of difficulties, and these require further exploration.